[English] 日本語
Yorodumi
- PDB-6x0a: X-ray structure of a chimeric ParDE toxin-antitoxin complex from ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6x0a
TitleX-ray structure of a chimeric ParDE toxin-antitoxin complex from Mesorhizobium opportunistum
Components
  • Plasmid stabilization system
  • Putative addiction module antidote protein, CopG/Arc/MetJ family chimera
KeywordsTOXIN / Toxin-antitoxin complex
Function / homology
Function and homology information


regulation of DNA-templated transcription
Similarity search - Function
Antitoxin ParD superfamily / Bacterial antitoxin of ParD toxin-antitoxin type II system and RHH / Antitoxin ParD / ParE toxin of type II toxin-antitoxin system, parDE / Toxin-antitoxin system, RelE/ParE toxin family / Toxin-antitoxin system, RelE/ParE toxin domain superfamily / Ribbon-helix-helix
Similarity search - Domain/homology
1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE / Putative addiction module antidote protein, CopG/Arc/MetJ family / Plasmid stabilization system / Addiction module antidote protein, CopG/Arc/MetJ family
Similarity search - Component
Biological speciesMesorhizobium opportunistum
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 Å
AuthorsLite, T.L. / Grant, R.A. / Laub, M.T.
Funding support United States, 2items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM082899 United States
CitationJournal: Elife / Year: 2020
Title: Uncovering the basis of protein-protein interaction specificity with a combinatorially complete library.
Authors: Lite, T.V. / Grant, R.A. / Nocedal, I. / Littlehale, M.L. / Guo, M.S. / Laub, M.T.
History
DepositionMay 15, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / software / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Plasmid stabilization system
B: Plasmid stabilization system
C: Plasmid stabilization system
D: Plasmid stabilization system
E: Plasmid stabilization system
F: Plasmid stabilization system
G: Plasmid stabilization system
H: Plasmid stabilization system
I: Plasmid stabilization system
J: Plasmid stabilization system
K: Plasmid stabilization system
L: Plasmid stabilization system
M: Plasmid stabilization system
N: Plasmid stabilization system
O: Plasmid stabilization system
P: Plasmid stabilization system
Q: Plasmid stabilization system
R: Plasmid stabilization system
a: Putative addiction module antidote protein, CopG/Arc/MetJ family chimera
b: Putative addiction module antidote protein, CopG/Arc/MetJ family chimera
c: Putative addiction module antidote protein, CopG/Arc/MetJ family chimera
d: Putative addiction module antidote protein, CopG/Arc/MetJ family chimera
e: Putative addiction module antidote protein, CopG/Arc/MetJ family chimera
f: Putative addiction module antidote protein, CopG/Arc/MetJ family chimera
g: Putative addiction module antidote protein, CopG/Arc/MetJ family chimera
h: Putative addiction module antidote protein, CopG/Arc/MetJ family chimera
i: Putative addiction module antidote protein, CopG/Arc/MetJ family chimera
j: Putative addiction module antidote protein, CopG/Arc/MetJ family chimera
k: Putative addiction module antidote protein, CopG/Arc/MetJ family chimera
l: Putative addiction module antidote protein, CopG/Arc/MetJ family chimera
m: Putative addiction module antidote protein, CopG/Arc/MetJ family chimera
n: Putative addiction module antidote protein, CopG/Arc/MetJ family chimera
o: Putative addiction module antidote protein, CopG/Arc/MetJ family chimera
p: Putative addiction module antidote protein, CopG/Arc/MetJ family chimera
q: Putative addiction module antidote protein, CopG/Arc/MetJ family chimera
r: Putative addiction module antidote protein, CopG/Arc/MetJ family chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)401,62346
Polymers400,00136
Non-polymers1,62210
Water00
1
A: Plasmid stabilization system
a: Putative addiction module antidote protein, CopG/Arc/MetJ family chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5474
Polymers22,2222
Non-polymers3242
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3250 Å2
ΔGint-21 kcal/mol
Surface area11780 Å2
MethodPISA
2
B: Plasmid stabilization system
b: Putative addiction module antidote protein, CopG/Arc/MetJ family chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3843
Polymers22,2222
Non-polymers1621
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-21 kcal/mol
Surface area12050 Å2
MethodPISA
3
C: Plasmid stabilization system
c: Putative addiction module antidote protein, CopG/Arc/MetJ family chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5474
Polymers22,2222
Non-polymers3242
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-22 kcal/mol
Surface area11960 Å2
MethodPISA
4
D: Plasmid stabilization system
d: Putative addiction module antidote protein, CopG/Arc/MetJ family chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5474
Polymers22,2222
Non-polymers3242
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-21 kcal/mol
Surface area11820 Å2
MethodPISA
5
E: Plasmid stabilization system
e: Putative addiction module antidote protein, CopG/Arc/MetJ family chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3843
Polymers22,2222
Non-polymers1621
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3200 Å2
ΔGint-20 kcal/mol
Surface area11000 Å2
MethodPISA
6
F: Plasmid stabilization system
f: Putative addiction module antidote protein, CopG/Arc/MetJ family chimera


Theoretical massNumber of molelcules
Total (without water)22,2222
Polymers22,2222
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint-21 kcal/mol
Surface area11750 Å2
MethodPISA
7
G: Plasmid stabilization system
g: Putative addiction module antidote protein, CopG/Arc/MetJ family chimera


Theoretical massNumber of molelcules
Total (without water)22,2222
Polymers22,2222
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3120 Å2
ΔGint-21 kcal/mol
Surface area12130 Å2
MethodPISA
8
H: Plasmid stabilization system
h: Putative addiction module antidote protein, CopG/Arc/MetJ family chimera


Theoretical massNumber of molelcules
Total (without water)22,2222
Polymers22,2222
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2980 Å2
ΔGint-23 kcal/mol
Surface area10710 Å2
MethodPISA
9
I: Plasmid stabilization system
i: Putative addiction module antidote protein, CopG/Arc/MetJ family chimera


Theoretical massNumber of molelcules
Total (without water)22,2222
Polymers22,2222
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2980 Å2
ΔGint-25 kcal/mol
Surface area11710 Å2
MethodPISA
10
J: Plasmid stabilization system
j: Putative addiction module antidote protein, CopG/Arc/MetJ family chimera


Theoretical massNumber of molelcules
Total (without water)22,2222
Polymers22,2222
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3080 Å2
ΔGint-24 kcal/mol
Surface area11240 Å2
MethodPISA
11
K: Plasmid stabilization system
k: Putative addiction module antidote protein, CopG/Arc/MetJ family chimera


Theoretical massNumber of molelcules
Total (without water)22,2222
Polymers22,2222
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-23 kcal/mol
Surface area11800 Å2
MethodPISA
12
L: Plasmid stabilization system
l: Putative addiction module antidote protein, CopG/Arc/MetJ family chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3843
Polymers22,2222
Non-polymers1621
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-23 kcal/mol
Surface area11860 Å2
MethodPISA
13
M: Plasmid stabilization system
m: Putative addiction module antidote protein, CopG/Arc/MetJ family chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3843
Polymers22,2222
Non-polymers1621
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-22 kcal/mol
Surface area11600 Å2
MethodPISA
14
N: Plasmid stabilization system
n: Putative addiction module antidote protein, CopG/Arc/MetJ family chimera


Theoretical massNumber of molelcules
Total (without water)22,2222
Polymers22,2222
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3050 Å2
ΔGint-25 kcal/mol
Surface area11690 Å2
MethodPISA
15
O: Plasmid stabilization system
o: Putative addiction module antidote protein, CopG/Arc/MetJ family chimera


Theoretical massNumber of molelcules
Total (without water)22,2222
Polymers22,2222
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint-25 kcal/mol
Surface area11070 Å2
MethodPISA
16
P: Plasmid stabilization system
p: Putative addiction module antidote protein, CopG/Arc/MetJ family chimera


Theoretical massNumber of molelcules
Total (without water)22,2222
Polymers22,2222
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3100 Å2
ΔGint-25 kcal/mol
Surface area11970 Å2
MethodPISA
17
Q: Plasmid stabilization system
q: Putative addiction module antidote protein, CopG/Arc/MetJ family chimera


Theoretical massNumber of molelcules
Total (without water)22,2222
Polymers22,2222
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3070 Å2
ΔGint-25 kcal/mol
Surface area11860 Å2
MethodPISA
18
R: Plasmid stabilization system
r: Putative addiction module antidote protein, CopG/Arc/MetJ family chimera


Theoretical massNumber of molelcules
Total (without water)22,2222
Polymers22,2222
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint-25 kcal/mol
Surface area11510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.540, 148.540, 195.270
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 5 through 92)
21(chain B and resid 5 through 92)
31(chain C and resid 5 through 92)
41(chain D and resid 5 through 92)
51(chain E and resid 5 through 92)
61(chain F and resid 5 through 92)
71(chain G and resid 5 through 92)
81(chain H and resid 5 through 92)
91chain I
101(chain J and resid 5 through 92)
111(chain K and resid 5 through 92)
121(chain L and resid 5 through 92)
131(chain M and resid 5 through 92)
141(chain N and resid 5 through 92)
151(chain O and resid 5 through 92)
161(chain P and resid 5 through 92)
171(chain Q and resid 5 through 92)
181(chain R and resid 5 through 92)
12(chain a and resid 11 through 89)
22(chain b and resid 11 through 89)
32(chain c and resid 11 through 89)
42(chain d and resid 11 through 89)
52chain e
62(chain f and resid 11 through 89)
72(chain g and resid 11 through 89)
82chain h
92(chain i and resid 11 through 89)
102(chain j and resid 11 through 89)
112(chain k and resid 11 through 89)
122(chain l and resid 11 through 89)
132(chain m and resid 11 through 89)
142(chain n and resid 11 through 89)
152(chain o and resid 11 through 89)
162(chain p and resid 11 through 89)
172(chain q and resid 11 through 89)
182(chain r and resid 11 through 89)

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGTHRTHR(chain A and resid 5 through 92)AA5 - 9219 - 106
21ARGARGTHRTHR(chain B and resid 5 through 92)BB5 - 9219 - 106
31ARGARGTHRTHR(chain C and resid 5 through 92)CC5 - 9219 - 106
41ARGARGTHRTHR(chain D and resid 5 through 92)DD5 - 9219 - 106
51ARGARGTHRTHR(chain E and resid 5 through 92)EE5 - 9219 - 106
61ARGARGTHRTHR(chain F and resid 5 through 92)FF5 - 9219 - 106
71ARGARGTHRTHR(chain G and resid 5 through 92)GG5 - 9219 - 106
81ARGARGTHRTHR(chain H and resid 5 through 92)HH5 - 9219 - 106
91ARGARGTHRTHRchain III5 - 9219 - 106
101ARGARGTHRTHR(chain J and resid 5 through 92)JJ5 - 9219 - 106
111ARGARGTHRTHR(chain K and resid 5 through 92)KK5 - 9219 - 106
121ARGARGTHRTHR(chain L and resid 5 through 92)LL5 - 9219 - 106
131ARGARGTHRTHR(chain M and resid 5 through 92)MM5 - 9219 - 106
141ARGARGTHRTHR(chain N and resid 5 through 92)NN5 - 9219 - 106
151ARGARGTHRTHR(chain O and resid 5 through 92)OO5 - 9219 - 106
161ARGARGTHRTHR(chain P and resid 5 through 92)PP5 - 9219 - 106
171ARGARGTHRTHR(chain Q and resid 5 through 92)QQ5 - 9219 - 106
181ARGARGTHRTHR(chain R and resid 5 through 92)RR5 - 9219 - 106
12VALVALILEILE(chain a and resid 11 through 89)aS11 - 8911 - 89
22VALVALILEILE(chain b and resid 11 through 89)bT11 - 8911 - 89
32VALVALILEILE(chain c and resid 11 through 89)cU11 - 8911 - 89
42VALVALILEILE(chain d and resid 11 through 89)dV11 - 8911 - 89
52VALVALILEILEchain eeW11 - 8911 - 89
62VALVALILEILE(chain f and resid 11 through 89)fX11 - 8911 - 89
72VALVALILEILE(chain g and resid 11 through 89)gY11 - 8911 - 89
82VALVALILEILEchain hhZ11 - 8911 - 89
92VALVALILEILE(chain i and resid 11 through 89)iAA11 - 8911 - 89
102VALVALILEILE(chain j and resid 11 through 89)jBA11 - 8911 - 89
112VALVALILEILE(chain k and resid 11 through 89)kCA11 - 8911 - 89
122VALVALILEILE(chain l and resid 11 through 89)lDA11 - 8911 - 89
132VALVALILEILE(chain m and resid 11 through 89)mEA11 - 8911 - 89
142VALVALILEILE(chain n and resid 11 through 89)nFA11 - 8911 - 89
152VALVALILEILE(chain o and resid 11 through 89)oGA11 - 8911 - 89
162VALVALILEILE(chain p and resid 11 through 89)pHA11 - 8911 - 89
172VALVALILEILE(chain q and resid 11 through 89)qIA11 - 8911 - 89
182VALVALILEILE(chain r and resid 11 through 89)rJA11 - 8911 - 89

NCS ensembles :
ID
1
2

-
Components

#1: Protein
Plasmid stabilization system


Mass: 11949.514 Da / Num. of mol.: 18
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mesorhizobium opportunistum (strain LMG 24607 / HAMBI 3007 / WSM2075) (bacteria)
Strain: LMG 24607 / HAMBI 3007 / WSM2075 / Gene: Mesop_5171 / Production host: Escherichia coli (E. coli) / References: UniProt: F7Y4W0
#2: Protein
Putative addiction module antidote protein, CopG/Arc/MetJ family chimera


Mass: 10272.750 Da / Num. of mol.: 18
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mesorhizobium opportunistum (strain LMG 24607 / HAMBI 3007 / WSM2075) (bacteria)
Strain: LMG 24607 / HAMBI 3007 / WSM2075 / Gene: Mesop_5599, Mesop_5170 / Production host: Escherichia coli (E. coli) / References: UniProt: F7YBW8, UniProt: F7Y4V9
#3: Chemical
ChemComp-P4G / 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE


Mass: 162.227 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C8H18O3
Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.11 Å3/Da / Density % sol: 60.44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2 M ammonium acetate, 0.1 M sodium citrate tribasic dihydrate pH 5.5, 24% v/v polyethylene glycol 400

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. obs: 105559 / % possible obs: 99 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.059 / Rrim(I) all: 0.131 / Χ2: 1.189 / Net I/σ(I): 5.1 / Num. measured all: 514447
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.9-2.953.80.91849300.7270.51.0510.64191.7
2.95-34.40.91251820.7540.4751.0320.64597.5
3-3.064.90.93753100.7610.4691.050.65299.8
3.06-3.125.10.82553030.8380.4030.920.68599.9
3.12-3.195.20.72853640.860.3540.8120.7199.9
3.19-3.275.10.61953330.8760.3020.6910.75199.8
3.27-3.3550.50152920.90.250.5610.81799.8
3.35-3.444.50.38552980.9240.2020.4360.91699.5
3.44-3.544.70.34353460.9320.1740.3860.94299.3
3.54-3.655.50.29252650.9620.1380.3231.0299.6
3.65-3.785.50.23452940.970.1110.261.15299.5
3.78-3.935.30.19952890.9740.0960.2221.22299
3.93-4.115.20.17452540.9770.0860.1951.30399.1
4.11-4.3350.14653060.9830.0740.1651.4399.2
4.33-4.64.70.1252870.9870.0630.1361.54299.3
4.6-4.954.40.10152490.9890.0560.1161.65698.5
4.95-5.454.30.09153050.9910.0520.1051.57999.1
5.45-6.235.30.09653190.9940.0480.1081.41399.9
6.23-7.834.90.06653250.9950.0350.0751.77799.8
7.83-304.60.05353080.9970.0270.062.98699.5

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHASERphasing
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6X09

6x09
PDB Unreleased entry


Resolution: 2.9→29.81 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 35.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2816 1998 1.9 %
Rwork0.2549 103338 -
obs0.2554 105336 98.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 353.26 Å2 / Biso mean: 133.0522 Å2 / Biso min: 50.44 Å2
Refinement stepCycle: final / Resolution: 2.9→29.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24667 0 290 0 24957
Biso mean--102.21 --
Num. residues----3158
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A7600X-RAY DIFFRACTION11.394TORSIONAL
12B7600X-RAY DIFFRACTION11.394TORSIONAL
13C7600X-RAY DIFFRACTION11.394TORSIONAL
14D7600X-RAY DIFFRACTION11.394TORSIONAL
15E7600X-RAY DIFFRACTION11.394TORSIONAL
16F7600X-RAY DIFFRACTION11.394TORSIONAL
17G7600X-RAY DIFFRACTION11.394TORSIONAL
18H7600X-RAY DIFFRACTION11.394TORSIONAL
19I7600X-RAY DIFFRACTION11.394TORSIONAL
110J7600X-RAY DIFFRACTION11.394TORSIONAL
111K7600X-RAY DIFFRACTION11.394TORSIONAL
112L7600X-RAY DIFFRACTION11.394TORSIONAL
113M7600X-RAY DIFFRACTION11.394TORSIONAL
114N7600X-RAY DIFFRACTION11.394TORSIONAL
115O7600X-RAY DIFFRACTION11.394TORSIONAL
116P7600X-RAY DIFFRACTION11.394TORSIONAL
117Q7600X-RAY DIFFRACTION11.394TORSIONAL
118R7600X-RAY DIFFRACTION11.394TORSIONAL
21a7191X-RAY DIFFRACTION11.394TORSIONAL
22b7191X-RAY DIFFRACTION11.394TORSIONAL
23c7191X-RAY DIFFRACTION11.394TORSIONAL
24d7191X-RAY DIFFRACTION11.394TORSIONAL
25e7191X-RAY DIFFRACTION11.394TORSIONAL
26f7191X-RAY DIFFRACTION11.394TORSIONAL
27g7191X-RAY DIFFRACTION11.394TORSIONAL
28h7191X-RAY DIFFRACTION11.394TORSIONAL
29i7191X-RAY DIFFRACTION11.394TORSIONAL
210j7191X-RAY DIFFRACTION11.394TORSIONAL
211k7191X-RAY DIFFRACTION11.394TORSIONAL
212l7191X-RAY DIFFRACTION11.394TORSIONAL
213m7191X-RAY DIFFRACTION11.394TORSIONAL
214n7191X-RAY DIFFRACTION11.394TORSIONAL
215o7191X-RAY DIFFRACTION11.394TORSIONAL
216p7191X-RAY DIFFRACTION11.394TORSIONAL
217q7191X-RAY DIFFRACTION11.394TORSIONAL
218r7191X-RAY DIFFRACTION11.394TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9-2.970.40721300.37626865699591
2.97-3.050.35741420.35847379752199
3.05-3.140.35831380.359674877625100
3.14-3.240.3571460.350274157561100
3.24-3.360.30941390.328374707609100
3.36-3.490.30131490.32817374752399
3.49-3.650.3311420.305574697611100
3.65-3.850.32651420.27467440758299
3.85-4.090.26421480.26387411755999
4.09-4.40.26521410.24957353749499
4.4-4.840.23461520.23117394754699
4.84-5.540.28961410.23467400754199
5.54-6.960.321440.26874837627100
6.96-29.810.22651440.18347398754299
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.4963-5.3476-1.71455.11620.34270.51940.61960.2652-0.72990.083-0.50170.32710.11630.1684-0.0050.7168-0.0063-0.00560.8244-0.12710.59132.3327-56.829222.6495
22.551-9.1393-3.03462.50667.88839.3519-0.1072-0.25611.37730.00271.2492-2.77810.0121.2406-0.79510.8199-0.14390.04260.811-0.08460.782240.7184-50.677723.3228
32.16345.02471.79064.70553.97432.2643-0.6599-0.46840.5549-0.06960.88020.1526-2.609-0.7636-0.13531.1670.08350.02830.68650.04630.796430.8609-35.313320.0789
47.1641-5.3917-3.84727.88836.61747.5179-0.4573-0.4135-0.13050.01650.12790.4438-0.93510.55920.5480.8648-0.0241-0.06870.7320.07440.403828.1458-41.67819.7647
51.1630.66874.02917.91434.21092.20120.20040.1718-0.1775-0.699-0.23440.0642-0.49850.08050.12710.6527-0.0887-0.10550.56580.03120.552228.5432-47.342715.0301
63.5579-0.032.4813.059-3.9532.7388-0.192-0.4129-0.0905-0.51130.1525-0.77090.4495-0.3997-0.13830.92610.10410.09120.7902-0.1090.495135.4387-26.4086-42.4915
72.92957.2137-3.58496.6957-6.60582.9380.8485-1.29891.95380.2494-0.5092.1364-1.1688-0.6972-0.64310.94860.14910.11040.946-0.0410.806726.5045-21.5295-40.848
84.719-2.0873-2.715410.2641-1.60432.1181-0.078-1.26090.00170.50040.40720.61172.0342-2.3191-0.30190.9968-0.2511-0.1631.25170.0170.738818.8181-39.1182-45.5223
94.08181.0695-0.16876.10260.71513.71560.0560.41550.0061-0.1149-0.2385-0.0164-0.0505-1.69860.12780.8133-0.0072-0.0710.9659-0.01470.486625.5513-34.2991-46.9352
105.09550.159-0.48853.94350.12713.50670.50830.4740.00130.6208-0.3421-0.02020.1994-0.9097-0.19561.0258-0.2502-0.0410.58370.00850.375333.206227.036523.0497
114.9518-5.4396-1.25677.95812.73636.3695-0.0879-0.1580.77161.54440.5593-1.5420.19530.8365-0.37770.9018-0.1717-0.1240.8167-0.01280.663241.021333.08222.866
123.4320.56310.63445.63360.70964.97370.21170.07230.37040.01360.0949-0.0265-0.6771-0.336-0.06920.9527-0.02510.05760.62420.03360.423328.288840.222318.1556
134.30956.04294.65571.97415.42365.66990.02111.73520.02110.99450.0084-0.237-0.6099-1.30720.48070.87150.1903-0.1310.8122-0.14331.146336.270963.104312.4637
146.24644.5127-0.45652.12357.51847.04380.04720.7431-0.2007-0.78280.7015-1.6212-1.18060.5118-0.88810.8389-0.1784-0.07220.72260.00770.575444.769852.28451.784
159.5072-5.0154-2.34044.71272.22675.5070.0198-0.3998-1.00620.9626-0.32971.02090.3318-0.08070.14690.8893-0.1613-0.03550.70030.14610.566840.086448.519112.1518
161.9857-2.7147-7.32752.0299-4.49157.62290.4694-2.38290.26153.3347-0.85350.75240.5544-1.3370.78331.6125-0.42170.30351.1865-0.16420.692640.385257.864526.7512
175.66182.59121.47223.2017-1.00465.20610.6816-1.69520.98940.6093-1.2575-0.2321-1.83260.20890.6551.4418-0.3565-0.31680.8801-0.05810.795552.118762.647923.0548
185.5070.3721.26863.39270.3755.5692-0.4821-1.15160.3763-0.01610.335-0.5056-0.2526-0.27620.64111.0005-0.3207-0.1791.030.0450.584850.714460.00818.5431
199.16055.11831.26318.45978.19152.63161.3044-1.1808-0.7555-1.3552-1.12131.7208-1.1758-1.26250.41961.1344-0.13440.00220.92180.07750.596744.296862.611617.4134
207.9839-7.3230.96142.6451-3.52655.31961.1732-1.09830.3769-0.59780.2255-0.5619-0.88010.0728-1.41340.8096-0.2069-0.10710.7484-0.15250.792944.012562.097113.1246
218.5045-1.0098-6.34258.60614.17921.97340.6484-1.7189-0.37222.2564-0.58810.7912.9416-0.25440.33911.1471-0.38270.03521.5012-0.00390.704964.153152.281211.4328
229.3708-1.61316.76673.5693-5.44471.99390.16171.36810.2853-0.4455-1.62630.53881.150.34351.39870.97660.05710.13980.2996-0.09741.286239.0067-20.437512.5046
239.55453.63761.24492.06349.51457.00730.0119-0.1905-0.177-0.6869-0.0031-1.6519-1.04680.53690.16520.8961-0.12260.09550.75870.09580.595446.8546-31.83322.1516
247.5848-8.6644-5.62782.12721.83342.17220.0826-0.4278-0.42230.6741-0.20680.87680.45510.58170.56271.0972-0.22030.0010.85090.11490.576541.5154-35.116412.406
251.87931.01540.63672.2450.08215.79190.459-1.81411.27252.3108-0.0491-0.214-0.25010.9858-0.16861.5961-0.3497-0.03550.8898-0.15361.016350.6661-21.716123.4475
269.0461-2.3049-4.04843.2382.10112.07770.6429-1.99-0.1164-0.21210.3881-0.8578-0.27930.0178-0.39221.0409-0.1439-0.16320.8510.05050.596951.2892-28.692918.6264
274.50160.25311.09295.80721.98043.69690.3379-0.1927-0.79350.626-0.82161.4211-1.3327-0.4486-0.10241.1804-0.2657-0.02820.92460.04620.797146.7408-21.426917.6587
282.6567-4.09571.63852.3847-2.82374.34271.2399-1.31891.02481.37270.3987-1.6875-1.4038-1.1737-0.55251.0605-0.16970.07410.7191-0.05861.020646.7124-21.81313.5157
294.1426-5.2733-1.48958.30454.53094.846-1.35640.2061-0.40340.68290.8194-0.16470.93460.94750.16191.0287-0.14140.13551.3443-0.02321.399365.929-33.313312.5022
306.2299-1.28750.54938.17860.4662-0.1383-0.30110.3894-0.08961.38910.33220.34060.9772-0.159-0.00850.7558-0.0415-0.04480.64640.02940.385439.742215.47170.5391
312.3048-5.2797-2.98967.5457.45568.33630.74220.67951.3971-0.9529-0.1057-2.0736-1.47730.3826-0.76460.9144-0.20060.06240.76410.16330.812248.499720.6494-1.3441
322.40792.6085-6.96499.1808-4.41938.7193-0.00870.2286-0.02850.09920.3737-1.98581.38451.4048-0.05560.8150.073-0.19131.0786-0.02180.979858.89765.45621.9338
338.8987-3.1233-1.62025.61712.11652.8626-0.13610.1401-0.36360.0182-0.41790.27440.31460.96470.44750.73880.0525-0.08260.6627-0.00720.481450.13916.86455.169
349.2348-0.60631.33141.55620.5765-0.14290.25670.1970.3652-0.67060.0693-0.03350.25660.046-0.430.81520.0179-0.020.5979-0.02870.438670.63890.93665.8531
352.31672.01318.00646.3352-0.43397.00960.57790.8677-1.5687-0.2002-0.03970.1081.56260.2474-0.23561.28090.01140.07080.7443-0.10040.552569.8124-9.358664.2115
365.4959-4.4148-7.36234.38366.16472.15080.3074-0.0561-1.1066-0.52860.18930.57340.0182-2.38530.52070.9221-0.2708-0.11021.19080.05880.936251.3442-9.244567.3653
374.920.7074-2.62755.1668-3.06245.3178-0.0077-0.03570.0823-0.1147-0.04760.22470.4091-1.18170.04480.64690.02-0.06460.9672-0.0350.496257.6492-2.5170.4687
389.07863.92113.28367.8688-6.07579.9987-1.1165-0.897-0.0709-0.1213-1.080.08651.01721.00451.54370.56280.14260.13590.8902-0.05670.8499-0.2209-41.899910.7003
397.1077-5.4728-3.26411.95271.80866.0720.0906-0.9055-0.0443-0.2408-0.028-0.0510.04091.22220.18390.64370.00530.0810.940.09370.6853-5.5859-29.327521.4294
403.9244-5.061-1.84049.12177.66792.390.00551.8617-0.3619-0.7042-0.98871.068-1.1506-1.69181.67880.6616-0.0091-0.07861.23030.11110.7979-11.2999-31.801311.2169
416.61250.0406-4.78298.49132.21667.21570.08041.47390.3201-2.10670.0581-0.9207-0.3816-0.4068-0.08630.77860.05960.20341.52090.18520.7844.6202-30.92780.0054
424.6861.52241.97950.4573-0.13527.2835-0.1737-0.52540.1938-0.14710.92630.16820.34320.9822-0.86950.7116-0.04240.0991.32080.09920.68011.4827-31.49265.4203
433.1617-4.6062-0.85482.04517.08182.0904-0.5490.21170.25880.47440.9368-0.05760.70440.2179-0.26420.82770.0330.19760.85980.14770.70692.4372-34.59919.9813
446.8793-4.68343.06675.20871.819.15860.09110.4487-0.23780.6198-2.2924-0.9186-0.6402-2.03681.48491.3436-0.552-0.09751.47210.08430.84083.408-12.160511.65
458.52563.409-2.72876.14841.72155.2628-1.86470.7066-0.6771-0.67481.3568-1.03492.2505-0.46350.60692.26540.1970.09941.28660.09111.002970.262919.50821.5349
466.41652.5201-3.66024.77410.89233.9533-2.70842.4179-0.9501-2.90330.41750.35163.1075-1.51810.88483.3589-0.81110.01181.96010.19461.193462.171719.441812.7672
476.48340.8397-0.90057.18822.09892.7275-1.1391.9175-0.7578-4.17121.0635-0.55990.84-0.92390.20323.1183-0.57670.26061.699-0.00841.080575.490324.40596.0093
486.2442-0.6112-0.76472.3634-0.95396.5137-0.51970.18480.9246-0.1168-0.2485-1.2917-0.446-0.6463-0.20491.30910.4916-0.18671.1516-0.15711.18627.2626-5.2036-76.0673
497.3464-0.3845-0.79653.0329-2.03227.11730.1595-0.12770.2272-0.4897-0.7005-0.4628-1.1720.34290.13031.25760.1432-0.1731.0682-0.12211.628319.5117-2.5722-77.4458
507.9131-0.9105-0.28917.06853.06422.1554-0.10850.92121.5368-0.24070.599-1.06040.32890.0903-0.00191.25020.276-0.12360.98410.2161.426617.7115-6.9656-86.1101
514.73762.69880.79493.1084-3.32738.62930.0261-0.95811.7849-0.314-0.4959-0.57210.88581.188-0.29821.66850.1694-0.33980.8833-0.19431.681518.8953-24.5933-75.3985
526.0197-1.14621.5136.9619-0.94294.4562-0.54360.0724-0.16330.33630.40840.87160.3139-0.35980.06881.1138-0.07950.14880.59270.0210.92821.9464-72.535861.7456
537.29051.7892-4.58994.8122-0.14272.0946-1.10311.64160.8623-2.30020.25732.6149-1.032-1.8201-0.0071.1444-0.101-0.36051.13470.03571.76-5.067-59.429648.6095
545.50190.6494-2.22655.1441-0.86097.39360.34810.2582-0.6964-0.1704-0.05551.29341.2408-1.04180.22071.2164-0.1417-0.26820.7182-0.00421.26-1.8023-65.954151.6215
558.96214.9691.01846.60662.03588.29480.195-1.03281.37060.6042-0.09550.5477-0.6922-0.4746-0.11431.12090.3869-0.0040.89230.13490.772514.4325-53.734657.1519
567.763.0921-1.19227.6421-1.59694.18470.41730.05990.1887-0.7570.0240.36720.4994-0.7207-0.51851.20230.194-0.09660.8698-0.06670.451638.2774-12.6823-64.7983
573.20011.3932-1.22396.4902-1.20427.48830.1646-0.00420.4195-0.1307-0.14220.1342-1.06121.01120.06741.0470.041-0.0430.7333-0.02070.476446.2355-1.3602-60.0483
585.99753.70741.05294.94170.57352.4423-0.54240.0604-0.39110.49330.4361-0.53070.1641.91220.10690.7135-0.12480.07970.8830.15251.175762.9145-42.8221-4.7077
592.79260.9808-0.70898.50796.41146.80420.0526-0.2431-0.52181.3608-0.540.1170.96321.15170.66490.9487-0.0854-0.12481.1170.14551.703362.0505-51.60381.1124
607.6551-9.55270.14362.1381-5.98518.1158-0.13382.8206-4.2761-1.0079-0.54440.42721.49480.110.59621.0654-0.33010.07791.4468-0.38272.218254.8169-60.0288-14.5491
618.21842.79952.2962.25819.47352.0796-0.09281.3756-2.19810.40570.2078-0.9960.4632-0.8607-0.71721.0457-0.11990.01520.9878-0.13351.431354.09-55.3229-10.2638
622.24221.9456-8.2922.08457.26718.4919-0.0737-0.42070.1245-0.95790.7521-1.31950.4052.484-1.33331.12580.21810.01131.2101-0.39011.5459.8212-55.5149-14.2065
633.3218-4.7483-1.32229.21970.31892.835-0.49333.6717-1.1224-0.7769-0.5842-1.68091.04760.14211.25820.78070.04480.30871.6708-0.39261.298261.1614-51.5633-13.3146
642.0254-4.4234-8.37542.0178-1.87232.012-1.0291-2.2493-0.1795-0.7781.14960.48312.2843-0.9994-0.14441.3199-0.1357-0.15021.15540.04230.672340.5782-44.3958-7.5901
653.32580.7891.75894.25691.39385.29590.10410.42510.8809-0.1853-0.15821.1078-0.96020.21780.34551.5622-0.351-0.22211.16040.06921.334463.190439.996932.3609
668.99530.3785-2.9142.3309-4.7932.13540.4228-1.05931.14151.207-0.40150.49870.1196-0.66210.36451.6973-0.32250.15590.9669-0.26671.860153.710135.824745.043
673.1018-0.40440.89912.23510.19946.74130.6945-0.99870.1866-0.5740.34460.5241-0.0034-0.1668-1.26041.7491-0.25550.02160.9017-0.17251.286359.348730.458239.9377
685.39040.5717-1.61955.4605-3.662.8553-0.1860.1738-0.5134-0.5955-0.1779-0.22950.4434-1.40530.53590.71180.1181-0.05461.098-0.02021.051711.5119-1.225-35.8367
695.34173.5936-0.67973.6991-1.17792.72240.24490.2176-1.5842-0.9381-0.6448-0.53271.22910.37550.3391.09750.296-0.06340.8754-0.11211.395614.432-13.212-36.6299
703.6214-0.97171.38487.82351.67763.8194-0.019-0.611-1.24210.9490.08070.92610.2153-0.51770.0140.67940.0567-0.02440.93670.17350.945719.4168-10.3395-28.3718
714.79820.5414-2.27992.66282.13243.4088-3.0090.7782-1.0483-2.42492.20040.93592.90160.27910.53653.5291-0.4730.11421.81720.29131.285865.4694-67.470917.2231
723.48141.80320.77894.41961.47893.1531-0.93162.2049-2.5357-1.82780.7143-0.42490.2118-0.07860.2073.2209-0.73560.4942.2064-0.0431.6276.9814-62.47161.6191
734.98321.56121.27554.42661.33152.939-1.06261.0795-0.5287-3.71271.5176-1.06230.0592-0.3840.21723.0591-0.39410.30631.6295-0.04551.191274.5924-62.54119.7449
746.0434-2.9632-1.66215.0034-0.69773.1613-1.5602-1.6264-0.51611.95061.34480.13131.67110.34780.34472.26640.3348-0.09211.35570.06681.0115.8734-23.0662-54.2625
752.93886.2176-4.39122.1345-6.52145.2211-1.0478-1.5083-2.012.0275-0.5328-1.7297-0.09311.38370.95592.2310.41050.12022.22280.23151.18280.4056-21.3431-47.6816
769.35893.2637-4.52856.37190.10152.6448-0.5-1.4173-0.6183-0.1318-0.9804-0.09851.03630.10481.91121.79360.2255-0.18511.25510.01840.9121-0.9478-16.9347-53.7281
774.4918-0.742-4.88853.61750.29496.6237-0.27430.14540.70590.1691-0.2781-1.32621.2787-0.45610.2721.60190.33360.21521.05050.18271.473873.7757-33.466599.8748
781.5456-3.0567-1.48597.46571.27788.3991-0.2461-0.82490.54720.01690.6208-2.3028-0.46890.8177-0.28081.31440.2901-0.04771.2511-0.03282.322980.731-22.7827103.2322
795.9902-0.5894-4.85173.83363.17015.77010.8706-0.24660.09940.9768-0.0092-0.85730.73421.3224-1.19831.64910.2979-0.18991.1560.14511.944775.1204-23.0964107.598
807.172-1.5423-5.009210.07442.6876.26371.10421.1148-0.4561-1.2485-0.5180.58190.303-1.0396-0.24981.02040.0403-0.32531.12770.1910.586923.2678-42.9034-24.8666
810.94060.7008-2.4816-0.292-0.79253.0528-0.4030.312-0.19930.0125-0.0779-0.13760.7265-1.18070.80190.897-0.0326-0.01191.0179-0.01720.485922.8926-48.61531.6293
822.2179-0.78230.08839.98258.08216.9656-0.59691.4288-0.65842.49341.59160.81231.13433.0028-0.60831.33690.1349-0.33981.3618-0.01110.790935.1846-64.533427.1119
832.73253.63322.20996.0105-0.49132.9885-0.41921.3572-0.88310.26180.5731-0.61060.05971.4544-0.46881.35530.0853-0.19330.9865-0.16930.725626.4684-41.5479-90.0219
84-1.3904-1.14671.3941-1.2718-1.28586.1615-0.52520.2558-0.0285-0.1334-0.405-0.21680.2755-0.94740.39261.7405-0.1118-0.03131.1574-0.0590.659131.1938-38.9023-69.0912
852.5342.4878-3.62853.1057-3.85065.6720.3909-0.6830.21960.0094-0.3431-0.2381-0.33370.0663-0.08690.89550.1184-0.04490.9756-0.10650.480238.922-25.882-37.2171
862.5453-0.5909-1.21285.399-1.67662.8528-0.07480.119-0.6049-0.63190.36670.71920.763-1.0124-0.07090.89470.0241-0.191.16790.00390.691923.351737.2939-25.125
870.71171.1325-0.70760.3901-3.50472.5059-0.06440.3205-0.1622-0.0344-0.23740.32320.6264-2.8159-0.13420.880.16240.00631.0874-0.03770.52220.992633.9708-0.8769
889.2385-2.18010.1143.6334.5055.09590.45830.5551-0.4481.5128-0.0004-0.0980.74080.815-0.31031.1413-0.2067-0.06841.13420.13740.527232.957622.896227.9723
893.1216-2.78373.23793.7284-1.08367.8557-0.7594-0.97320.93290.05770.381-0.2454-0.2469-0.52681.39011.7142-0.4354-0.42042.0971-0.63882.885290.863765.867513.7824
908.8221-5.90041.94736.75345.42611.9936-0.399-0.24890.32970.137-0.239-0.8690.0292-0.52571.27371.5509-0.16010.11872.28020.27532.569295.126649.60514.4959
913.7445-0.3299-1.17971.04440.70153.55790.5233-0.76751.7228-0.8301-0.0282-1.75-0.61731.6841-0.18361.3165-0.54620.09791.65290.10751.590971.142360.63729.0641
923.3146-0.0368-0.55212.09812.00944.71930.48170.6995-0.362-0.4554-1.26910.0058-2.284-2.9050.52631.1623-0.0666-0.04870.92740.01560.761337.08655.29680.931
932.3682-0.5801-3.76810.88180.36286.5696-1.2114-4.01861.4602-0.46341.3084-0.29452.27823.0374-0.3571.3416-0.09540.02533.50460.06892.774696.3943-38.155816.1275
941.6987-0.583-1.8455-0.0196-1.09252.20740.4707-0.10490.4017-0.7419-0.1948-2.0068-0.53691.30830.20621.1321-0.52760.05961.4488-0.22452.133273.6437-25.866510.0368
952.9342-0.3857-1.48982.6229-0.98653.3122-0.31330.2695-0.5143-0.955-0.7022-0.192-1.8594-1.3637-0.01441.1483-0.12340.00731.047-0.00330.83739.3751-28.28251.0859
963.8699-0.6611.04892.2393-1.05752.6919-0.3849-0.51410.37290.0596-0.00360.5135-0.2694-0.68690.41491.28520.0839-0.20011.0473-0.02640.749750.85642.570348.8693
97-0.26350.81072.2528-0.3824-2.64092.5233-0.5198-0.0620.22380.0784-0.53450.41180.658-0.1830.19281.1710.0438-0.07491.0031-0.08640.652344.82312.011624.4548
984.44041.3947-0.70260.82320.21639.7870.235-0.10520.04260.3955-0.37090.3440.3869-0.90520.35240.84190.04580.08161.0673-0.03720.607741.19415.7535-6.5967
992.17871.69991.9572.32386.46672.22490.75040.1086-1.4648-0.5168-0.94321.2444-2.16831.29070.04761.0535-0.1153-0.0010.94370.23920.73433.473421.0986-3.5965
1003.55730.8313-2.10094.7511-3.22535.3210.3761-0.26110.8731-0.176-0.4899-0.4747-0.32910.62450.31661.12750.07040.13591.37890.01411.013953.98250.8081113.7868
1010.6612-0.968-3.88860.8013-2.09056.9157-0.4069-0.43920.08390.5554-0.1906-0.2027-1.7717-0.90580.16791.0014-0.0225-0.05241.2402-0.02840.619856.75655.131489.5589
1022.4745-0.80624.7593.64950.66772.7425-0.52080.40580.35-0.41120.4264-0.28040.27910.32270.47211.0284-0.02010.13390.9032-0.03140.585672.93983.56460.5564
1034.9683-1.09792.24871.885-2.25322.7635-1.3837-0.15622.4037-2.0427-0.3566-1.1911-2.49970.54391.4272.2034-0.3749-0.30331.20050.1322.379415.216215.65198.1736
1040.34121.27051.52994.33560.01082.3475-0.4351-0.25950.87931.75670.7188-2.5115-0.84691.4824-0.06731.051-0.46180.03561.7715-0.08221.891913.6767-9.59714.0779
1051.9038-0.9951-2.01374.49261.28283.2163-1.0106-0.62040.06241.20950.25960.11282.10041.19820.27780.78620.1289-0.05160.9911-0.06770.7669-6.5551-37.625422.3875
1066.2791-1.6012-1.18439.4074-2.3943.89140.2297-0.54960.96280.0243-0.869-2.6057-0.17721.1190.72821.0095-0.33890.07531.8027-0.02091.560182.786351.498714.7198
1077.55862.3685-1.48122.28880.39223.8263-0.08841.55090.159-2.37330.6379-1.63381.0947-0.7161-0.95922.3162-0.28810.21441.1076-0.08331.347769.67411.982322.0003
1082.25824.00521.1689.2449-3.4978.05111.39390.1858-2.48931.46420.0122-1.21741.591-0.3384-0.42551.51860.4237-0.33381.6810.08831.442232.5454-49.2666-75.4257
1091.8219-0.0662-0.20480.94691.795-0.3519-0.20760.01480.8503-0.18190.1825-0.29690.2225-0.2827-0.06561.51210.3829-0.04451.11190.09420.972911.893-17.9195-80.9461
1107.9863-0.33791.63237.31921.35936.39880.2213-0.91061.32620.95210.4126-0.5176-3.85761.7416-0.21691.623-0.33890.16961.0884-0.24981.03227.0753-29.125152.8817
1111.25720.1347-0.30784.1296-0.57582.8021-0.00420.2601-0.4170.2501-0.0750.39820.54680.17890.10610.9375-0.1131-0.04610.73470.02310.700911.9471-63.661252.4036
1122.20940.6355-0.71334.84760.53012.98130.4405-0.7801-0.86920.1149-0.2118-0.2409-0.15541.99460.00370.8336-0.0129-0.04881.1164-0.24210.523150.0534-2.3455-16.5046
113-0.25240.00220.18490.43562.50612.4795-0.3914-0.1839-0.189-0.1009-0.277-0.00791.18362.2709-0.06040.94290.01770.04691.2352-0.01070.636653.635-6.8457-41.5786
1146.65252.39631.35133.0336-3.7555.34320.312-0.5869-0.589-1.5648-0.2316-0.02310.4364-0.6651-0.23041.26790.1868-0.1651.0364-0.06820.690141.5763-19.2543-70.028
1154.3772-0.6362-3.30698.58395.66472.3766-0.06070.457-0.1232-0.2374-0.20650.80530.6482-2.70970.05940.80360.0103-0.04191.37310.07120.670913.2277-42.104-12.285
1168.91060.52950.19420.2477-2.08570.6231.2453-0.3181-0.0033-0.7897-0.2958-0.1395-0.99950.2823-0.42361.0492-0.09940.05011.2709-0.15890.561638.5659-42.6665-16.8467
1173.46761.21671.17513.2913-0.15343.69620.2041-0.4367-1.49190.009-0.1202-1.3117-1.10170.7011-0.00880.6787-0.16430.01121.52840.13721.410869.155-41.8003-4.9519
1187.15881.82210.73586.39132.23922.08020.6156-0.3142-0.73080.0232-0.19030.22080.1479-0.3918-0.15331.173-0.2399-0.01420.9087-0.01630.800445.5515-8.12935.2717
1193.99495.0512.18448.87052.22312.26360.06440.27850.59391.57210.4262-0.1634-0.41420.8382-0.08611.5358-0.19690.02270.9193-0.0020.760658.607713.770542.4157
1201.1024-0.8093-1.40331.6968-1.63112.47491.0388-0.76120.67080.0858-0.2909-0.2718-0.54690.5788-0.49241.8277-0.3613-0.18320.991-0.01211.853271.488843.450433.5318
1214.8938-2.08340.73124.9833-6.00578.62050.1921-0.1688-0.3613-0.3120.1472-0.5738-0.19620.7035-0.52180.75180.0247-0.08841.6025-0.10610.614261.9087-1.1223-31.404
1228.19530.8832-0.37481.15060.35612.50071.0313-0.59210.25330.427-0.4670.4558-0.33260.0341-0.50960.7331-0.01280.0551.06250.08320.614230.8923-1.6451-25.0052
1232.27865.22511.02792.0104-0.09327.024-0.79830.5836-0.11541.31541.72172.4385-0.895-0.7634-1.20690.70740.3064-0.08491.5803-0.30611.66395.65914.2013-40.7135
1242.8751-3.2684.65283.8672-4.86597.5131.12181.03330.87240.2005-1.38040.42290.03051.48991.4331.9877-0.12510.43532.74930.27682.396196.0558-25.761616.7237
1253.758-3.46682.67937.6217-0.08322.883-0.1908-0.33690.91740.7991-0.91440.5711-0.61160.40881.20431.6905-0.29780.04042.4989-0.12852.401381.2689-16.101613.9551
1265.45931.327-2.3621.4631-2.33733.61751.3404-1.30411.8638-0.1718-0.4378-0.2776-2.05390.4836-0.57841.9028-0.5010.15861.8363-0.69542.239480.5256-19.023922.8139
1274.87572.8219-2.38496.8383-5.28744.6872-0.3904-0.5805-0.3242-0.4178-0.4695-1.46531.46010.48840.8351.4731-0.34540.23221.8164-0.10221.459984.473-46.129116.5132
1287.34372.4065-3.29315.2732-2.6196.8138-2.01510.0195-0.8428-2.72530.3415-1.11722.13060.21491.68043.65380.24911.281.6340.03482.215175.947-75.687813.9908
1298.01682.4544-0.75035.4269-4.90367.8692-0.3713-0.3291-0.1382-3.224-0.06881.74781.4018-1.4930.90592.0628-0.2056-0.29061.39620.19541.149564.2495-72.921926.9935
1303.07674.96292.43117.16334.02414.8226-0.0937-0.28240.6644-0.426-0.93561.60810.66451.29150.76961.59820.58120.08342.17470.21552.0512-10.514723.2291-57.1064
1310.9787-2.11970.47012.8332.06894.8234-0.4989-0.12910.50381.13650.6224-0.10910.9645-0.39730.06141.19630.06830.13821.45060.15261.6117-3.973-14.0507-59.6776
1326.76413.67632.57078.03660.35085.582-0.72091.38281.6784-0.78260.5320.9833-1.8191-0.9540.68771.4550.1349-0.00381.46750.26521.322148.614710.8524100.4911
1331.61380.779-1.27122.40680.75350.8672-0.4571-0.6067-0.40281.22350.4745-0.89840.74770.2860.05481.53810.436-0.10741.17330.01231.231765.4056-22.9725104.7226
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 24 )A2 - 24
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 43 )A25 - 43
3X-RAY DIFFRACTION3chain 'A' and (resid 44 through 53 )A44 - 53
4X-RAY DIFFRACTION4chain 'A' and (resid 54 through 76 )A54 - 76
5X-RAY DIFFRACTION5chain 'A' and (resid 77 through 92 )A77 - 92
6X-RAY DIFFRACTION6chain 'B' and (resid 2 through 24 )B2 - 24
7X-RAY DIFFRACTION7chain 'B' and (resid 25 through 43 )B25 - 43
8X-RAY DIFFRACTION8chain 'B' and (resid 44 through 58 )B44 - 58
9X-RAY DIFFRACTION9chain 'B' and (resid 59 through 92 )B59 - 92
10X-RAY DIFFRACTION10chain 'C' and (resid 1 through 24 )C1 - 24
11X-RAY DIFFRACTION11chain 'C' and (resid 25 through 43 )C25 - 43
12X-RAY DIFFRACTION12chain 'C' and (resid 44 through 92 )C44 - 92
13X-RAY DIFFRACTION13chain 'D' and (resid 2 through 6 )D2 - 6
14X-RAY DIFFRACTION14chain 'D' and (resid 7 through 24 )D7 - 24
15X-RAY DIFFRACTION15chain 'D' and (resid 25 through 43 )D25 - 43
16X-RAY DIFFRACTION16chain 'D' and (resid 44 through 48 )D44 - 48
17X-RAY DIFFRACTION17chain 'D' and (resid 49 through 53 )D49 - 53
18X-RAY DIFFRACTION18chain 'D' and (resid 54 through 66 )D54 - 66
19X-RAY DIFFRACTION19chain 'D' and (resid 67 through 76 )D67 - 76
20X-RAY DIFFRACTION20chain 'D' and (resid 77 through 85 )D77 - 85
21X-RAY DIFFRACTION21chain 'D' and (resid 86 through 92 )D86 - 92
22X-RAY DIFFRACTION22chain 'E' and (resid 2 through 6 )E2 - 6
23X-RAY DIFFRACTION23chain 'E' and (resid 7 through 24 )E7 - 24
24X-RAY DIFFRACTION24chain 'E' and (resid 25 through 43 )E25 - 43
25X-RAY DIFFRACTION25chain 'E' and (resid 44 through 58 )E44 - 58
26X-RAY DIFFRACTION26chain 'E' and (resid 59 through 66 )E59 - 66
27X-RAY DIFFRACTION27chain 'E' and (resid 67 through 76 )E67 - 76
28X-RAY DIFFRACTION28chain 'E' and (resid 77 through 85 )E77 - 85
29X-RAY DIFFRACTION29chain 'E' and (resid 86 through 92 )E86 - 92
30X-RAY DIFFRACTION30chain 'F' and (resid 2 through 24 )F2 - 24
31X-RAY DIFFRACTION31chain 'F' and (resid 25 through 43 )F25 - 43
32X-RAY DIFFRACTION32chain 'F' and (resid 44 through 53 )F44 - 53
33X-RAY DIFFRACTION33chain 'F' and (resid 54 through 92 )F54 - 92
34X-RAY DIFFRACTION34chain 'G' and (resid 2 through 24 )G2 - 24
35X-RAY DIFFRACTION35chain 'G' and (resid 25 through 43 )G25 - 43
36X-RAY DIFFRACTION36chain 'G' and (resid 44 through 53 )G44 - 53
37X-RAY DIFFRACTION37chain 'G' and (resid 54 through 92 )G54 - 92
38X-RAY DIFFRACTION38chain 'H' and (resid 2 through 6 )H2 - 6
39X-RAY DIFFRACTION39chain 'H' and (resid 7 through 24 )H7 - 24
40X-RAY DIFFRACTION40chain 'H' and (resid 25 through 43 )H25 - 43
41X-RAY DIFFRACTION41chain 'H' and (resid 44 through 58 )H44 - 58
42X-RAY DIFFRACTION42chain 'H' and (resid 59 through 76 )H59 - 76
43X-RAY DIFFRACTION43chain 'H' and (resid 77 through 85 )H77 - 85
44X-RAY DIFFRACTION44chain 'H' and (resid 86 through 92 )H86 - 92
45X-RAY DIFFRACTION45chain 'I' and (resid 5 through 24 )I5 - 24
46X-RAY DIFFRACTION46chain 'I' and (resid 25 through 43 )I25 - 43
47X-RAY DIFFRACTION47chain 'I' and (resid 44 through 92 )I44 - 92
48X-RAY DIFFRACTION48chain 'J' and (resid 2 through 24 )J2 - 24
49X-RAY DIFFRACTION49chain 'J' and (resid 25 through 53 )J25 - 53
50X-RAY DIFFRACTION50chain 'J' and (resid 54 through 85 )J54 - 85
51X-RAY DIFFRACTION51chain 'J' and (resid 86 through 92 )J86 - 92
52X-RAY DIFFRACTION52chain 'K' and (resid 2 through 43 )K2 - 43
53X-RAY DIFFRACTION53chain 'K' and (resid 44 through 58 )K44 - 58
54X-RAY DIFFRACTION54chain 'K' and (resid 59 through 85 )K59 - 85
55X-RAY DIFFRACTION55chain 'K' and (resid 86 through 92 )K86 - 92
56X-RAY DIFFRACTION56chain 'L' and (resid 2 through 43 )L2 - 43
57X-RAY DIFFRACTION57chain 'L' and (resid 44 through 92 )L44 - 92
58X-RAY DIFFRACTION58chain 'M' and (resid 3 through 24 )M3 - 24
59X-RAY DIFFRACTION59chain 'M' and (resid 25 through 42 )M25 - 42
60X-RAY DIFFRACTION60chain 'M' and (resid 43 through 57 )M43 - 57
61X-RAY DIFFRACTION61chain 'M' and (resid 58 through 66 )M58 - 66
62X-RAY DIFFRACTION62chain 'M' and (resid 67 through 76 )M67 - 76
63X-RAY DIFFRACTION63chain 'M' and (resid 77 through 85 )M77 - 85
64X-RAY DIFFRACTION64chain 'M' and (resid 86 through 92 )M86 - 92
65X-RAY DIFFRACTION65chain 'N' and (resid 2 through 43 )N2 - 43
66X-RAY DIFFRACTION66chain 'N' and (resid 44 through 76 )N44 - 76
67X-RAY DIFFRACTION67chain 'N' and (resid 77 through 92 )N77 - 92
68X-RAY DIFFRACTION68chain 'O' and (resid 2 through 24 )O2 - 24
69X-RAY DIFFRACTION69chain 'O' and (resid 25 through 53 )O25 - 53
70X-RAY DIFFRACTION70chain 'O' and (resid 54 through 92 )O54 - 92
71X-RAY DIFFRACTION71chain 'P' and (resid 2 through 43 )P2 - 43
72X-RAY DIFFRACTION72chain 'P' and (resid 44 through 58 )P44 - 58
73X-RAY DIFFRACTION73chain 'P' and (resid 59 through 92 )P59 - 92
74X-RAY DIFFRACTION74chain 'Q' and (resid 2 through 58 )Q2 - 58
75X-RAY DIFFRACTION75chain 'Q' and (resid 59 through 76 )Q59 - 76
76X-RAY DIFFRACTION76chain 'Q' and (resid 77 through 92 )Q77 - 92
77X-RAY DIFFRACTION77chain 'R' and (resid 2 through 24 )R2 - 24
78X-RAY DIFFRACTION78chain 'R' and (resid 25 through 66 )R25 - 66
79X-RAY DIFFRACTION79chain 'R' and (resid 67 through 92 )R67 - 92
80X-RAY DIFFRACTION80chain 'a' and (resid 3 through 24 )a3 - 24
81X-RAY DIFFRACTION81chain 'a' and (resid 25 through 73 )a25 - 73
82X-RAY DIFFRACTION82chain 'a' and (resid 74 through 89 )a74 - 89
83X-RAY DIFFRACTION83chain 'b' and (resid 3 through 25 )b3 - 25
84X-RAY DIFFRACTION84chain 'b' and (resid 26 through 64 )b26 - 64
85X-RAY DIFFRACTION85chain 'b' and (resid 65 through 89 )b65 - 89
86X-RAY DIFFRACTION86chain 'c' and (resid 3 through 30 )c3 - 30
87X-RAY DIFFRACTION87chain 'c' and (resid 31 through 64 )c31 - 64
88X-RAY DIFFRACTION88chain 'c' and (resid 65 through 89 )c65 - 89
89X-RAY DIFFRACTION89chain 'd' and (resid 5 through 12 )d5 - 12
90X-RAY DIFFRACTION90chain 'd' and (resid 13 through 25 )d13 - 25
91X-RAY DIFFRACTION91chain 'd' and (resid 26 through 65 )d26 - 65
92X-RAY DIFFRACTION92chain 'd' and (resid 66 through 89 )d66 - 89
93X-RAY DIFFRACTION93chain 'e' and (resid 11 through 25 )e11 - 25
94X-RAY DIFFRACTION94chain 'e' and (resid 26 through 65 )e26 - 65
95X-RAY DIFFRACTION95chain 'e' and (resid 66 through 89 )e66 - 89
96X-RAY DIFFRACTION96chain 'f' and (resid 5 through 30 )f5 - 30
97X-RAY DIFFRACTION97chain 'f' and (resid 31 through 64 )f31 - 64
98X-RAY DIFFRACTION98chain 'f' and (resid 65 through 73 )f65 - 73
99X-RAY DIFFRACTION99chain 'f' and (resid 74 through 89 )f74 - 89
100X-RAY DIFFRACTION100chain 'g' and (resid 4 through 30 )g4 - 30
101X-RAY DIFFRACTION101chain 'g' and (resid 31 through 64 )g31 - 64
102X-RAY DIFFRACTION102chain 'g' and (resid 65 through 89 )g65 - 89
103X-RAY DIFFRACTION103chain 'h' and (resid 11 through 24 )h11 - 24
104X-RAY DIFFRACTION104chain 'h' and (resid 25 through 65 )h25 - 65
105X-RAY DIFFRACTION105chain 'h' and (resid 66 through 89 )h66 - 89
106X-RAY DIFFRACTION106chain 'i' and (resid 7 through 65 )i7 - 65
107X-RAY DIFFRACTION107chain 'i' and (resid 66 through 89 )i66 - 89
108X-RAY DIFFRACTION108chain 'j' and (resid 7 through 30 )j7 - 30
109X-RAY DIFFRACTION109chain 'j' and (resid 31 through 89 )j31 - 89
110X-RAY DIFFRACTION110chain 'k' and (resid 5 through 30 )k5 - 30
111X-RAY DIFFRACTION111chain 'k' and (resid 31 through 89 )k31 - 89
112X-RAY DIFFRACTION112chain 'l' and (resid 4 through 30 )l4 - 30
113X-RAY DIFFRACTION113chain 'l' and (resid 31 through 65 )l31 - 65
114X-RAY DIFFRACTION114chain 'l' and (resid 66 through 89 )l66 - 89
115X-RAY DIFFRACTION115chain 'm' and (resid 5 through 31 )m5 - 31
116X-RAY DIFFRACTION116chain 'm' and (resid 32 through 64 )m32 - 64
117X-RAY DIFFRACTION117chain 'm' and (resid 65 through 89 )m65 - 89
118X-RAY DIFFRACTION118chain 'n' and (resid 5 through 30 )n5 - 30
119X-RAY DIFFRACTION119chain 'n' and (resid 31 through 65 )n31 - 65
120X-RAY DIFFRACTION120chain 'n' and (resid 66 through 89 )n66 - 89
121X-RAY DIFFRACTION121chain 'o' and (resid 7 through 30 )o7 - 30
122X-RAY DIFFRACTION122chain 'o' and (resid 31 through 73 )o31 - 73
123X-RAY DIFFRACTION123chain 'o' and (resid 74 through 89 )o74 - 89
124X-RAY DIFFRACTION124chain 'p' and (resid 3 through 12 )p3 - 12
125X-RAY DIFFRACTION125chain 'p' and (resid 13 through 24 )p13 - 24
126X-RAY DIFFRACTION126chain 'p' and (resid 25 through 31 )p25 - 31
127X-RAY DIFFRACTION127chain 'p' and (resid 32 through 64 )p32 - 64
128X-RAY DIFFRACTION128chain 'p' and (resid 65 through 73 )p65 - 73
129X-RAY DIFFRACTION129chain 'p' and (resid 74 through 89 )p74 - 89
130X-RAY DIFFRACTION130chain 'q' and (resid 4 through 30 )q4 - 30
131X-RAY DIFFRACTION131chain 'q' and (resid 31 through 89 )q31 - 89
132X-RAY DIFFRACTION132chain 'r' and (resid 5 through 30 )r5 - 30
133X-RAY DIFFRACTION133chain 'r' and (resid 31 through 89 )r31 - 89

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more