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- PDB-7ap5: Crystal structure of phycoerythrin from cyanobacterium Nostoc sp.... -

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Basic information

Entry
Database: PDB / ID: 7ap5
TitleCrystal structure of phycoerythrin from cyanobacterium Nostoc sp. WR13 contains multiple stacks of hexameric assemblies which resemble the rods of phycobilisome.
Components
  • Alpha subunit of cyanobacterial protein phycoerythrin
  • Beta subunit of cyanobacterial protein phycoerythrin
KeywordsPHOTOSYNTHESIS / Allophycocyanin crystal structure Phycobilisome Phycobiliproteins Phycocyanobilin chromophore Light harvesting complex Cyanobacterium Nostoc sp. WR13
Function / homologyNITRATE ION / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL / PHYCOERYTHROBILIN / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / PHOSPHATE ION / dodecaethylene glycol monomethyl ether
Function and homology information
Biological speciesNostoc sp. WR13 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.131 Å
AuthorsPatel, H.M. / Roszak, A.W. / Cogdell, R.J. / Madamwar, D. / Liu, H. / Gross, M.L. / Blankenship, R.E.
Funding support United States, India, 3items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-SC0001035 (Office of Basic Energy Sciences) United States
Department of Biotechnology (DBT, India)BT/PR15686/AAQ/3/811/2016 (UGC-BSR Faculty Fellowship) India
Department of Biotechnology (DBT, India)BT/IN/UK/DBT-BC/2017-18 (Newton-Bhabha fellowship) India
CitationJournal: To Be Published
Title: The crystal stacks of hexameric assemblies of phycoerythrin from cyanobacterium Nostoc sp. WR13 resemble rods of phycobilisome
Authors: Patel, H.M. / Roszak, A.W. / Liu, H. / Gross, M.L. / Blankenship, R.E. / Madamwar, D. / Cogdell, R.J.
History
DepositionOct 15, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 17, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Alpha subunit of cyanobacterial protein phycoerythrin
BBB: Beta subunit of cyanobacterial protein phycoerythrin
CCC: Alpha subunit of cyanobacterial protein phycoerythrin
DDD: Beta subunit of cyanobacterial protein phycoerythrin
EEE: Alpha subunit of cyanobacterial protein phycoerythrin
FFF: Beta subunit of cyanobacterial protein phycoerythrin
GGG: Alpha subunit of cyanobacterial protein phycoerythrin
HHH: Beta subunit of cyanobacterial protein phycoerythrin
III: Alpha subunit of cyanobacterial protein phycoerythrin
JJJ: Beta subunit of cyanobacterial protein phycoerythrin
KKK: Alpha subunit of cyanobacterial protein phycoerythrin
LLL: Beta subunit of cyanobacterial protein phycoerythrin
MMM: Alpha subunit of cyanobacterial protein phycoerythrin
NNN: Beta subunit of cyanobacterial protein phycoerythrin
OOO: Alpha subunit of cyanobacterial protein phycoerythrin
PPP: Beta subunit of cyanobacterial protein phycoerythrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)355,846336
Polymers294,75016
Non-polymers61,096320
Water24,5901365
1
AAA: Alpha subunit of cyanobacterial protein phycoerythrin
BBB: Beta subunit of cyanobacterial protein phycoerythrin
CCC: Alpha subunit of cyanobacterial protein phycoerythrin
DDD: Beta subunit of cyanobacterial protein phycoerythrin
EEE: Alpha subunit of cyanobacterial protein phycoerythrin
FFF: Beta subunit of cyanobacterial protein phycoerythrin
GGG: Alpha subunit of cyanobacterial protein phycoerythrin
HHH: Beta subunit of cyanobacterial protein phycoerythrin
III: Alpha subunit of cyanobacterial protein phycoerythrin
JJJ: Beta subunit of cyanobacterial protein phycoerythrin
KKK: Alpha subunit of cyanobacterial protein phycoerythrin
LLL: Beta subunit of cyanobacterial protein phycoerythrin
MMM: Alpha subunit of cyanobacterial protein phycoerythrin
NNN: Beta subunit of cyanobacterial protein phycoerythrin
OOO: Alpha subunit of cyanobacterial protein phycoerythrin
PPP: Beta subunit of cyanobacterial protein phycoerythrin
hetero molecules

AAA: Alpha subunit of cyanobacterial protein phycoerythrin
BBB: Beta subunit of cyanobacterial protein phycoerythrin
CCC: Alpha subunit of cyanobacterial protein phycoerythrin
DDD: Beta subunit of cyanobacterial protein phycoerythrin
EEE: Alpha subunit of cyanobacterial protein phycoerythrin
FFF: Beta subunit of cyanobacterial protein phycoerythrin
GGG: Alpha subunit of cyanobacterial protein phycoerythrin
HHH: Beta subunit of cyanobacterial protein phycoerythrin
III: Alpha subunit of cyanobacterial protein phycoerythrin
JJJ: Beta subunit of cyanobacterial protein phycoerythrin
KKK: Alpha subunit of cyanobacterial protein phycoerythrin
LLL: Beta subunit of cyanobacterial protein phycoerythrin
MMM: Alpha subunit of cyanobacterial protein phycoerythrin
NNN: Beta subunit of cyanobacterial protein phycoerythrin
OOO: Alpha subunit of cyanobacterial protein phycoerythrin
PPP: Beta subunit of cyanobacterial protein phycoerythrin
hetero molecules

AAA: Alpha subunit of cyanobacterial protein phycoerythrin
BBB: Beta subunit of cyanobacterial protein phycoerythrin
CCC: Alpha subunit of cyanobacterial protein phycoerythrin
DDD: Beta subunit of cyanobacterial protein phycoerythrin
EEE: Alpha subunit of cyanobacterial protein phycoerythrin
FFF: Beta subunit of cyanobacterial protein phycoerythrin
GGG: Alpha subunit of cyanobacterial protein phycoerythrin
HHH: Beta subunit of cyanobacterial protein phycoerythrin
III: Alpha subunit of cyanobacterial protein phycoerythrin
JJJ: Beta subunit of cyanobacterial protein phycoerythrin
KKK: Alpha subunit of cyanobacterial protein phycoerythrin
LLL: Beta subunit of cyanobacterial protein phycoerythrin
MMM: Alpha subunit of cyanobacterial protein phycoerythrin
NNN: Beta subunit of cyanobacterial protein phycoerythrin
OOO: Alpha subunit of cyanobacterial protein phycoerythrin
PPP: Beta subunit of cyanobacterial protein phycoerythrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,067,5381008
Polymers884,25148
Non-polymers183,287960
Water86548
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Unit cell
Length a, b, c (Å)192.759, 192.759, 524.486
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11AAA-213-

PEG

21AAA-214-

PO4

31AAA-370-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11Chains AAA CCC
22Chains AAA EEE
33Chains AAA GGG
44Chains AAA III
55Chains AAA KKK
66Chains AAA MMM
77Chains AAA OOO
88Chains BBB DDD
99Chains BBB FFF
1010Chains BBB HHH
1111Chains BBB JJJ
1212Chains BBB LLL
1313Chains BBB NNN
1414Chains BBB PPP
1515Chains CCC EEE
1616Chains CCC GGG
1717Chains CCC III
1818Chains CCC KKK
1919Chains CCC MMM
2020Chains CCC OOO
2121Chains DDD FFF
2222Chains DDD HHH
2323Chains DDD JJJ
2424Chains DDD LLL
2525Chains DDD NNN
2626Chains DDD PPP
2727Chains EEE GGG
2828Chains EEE III
2929Chains EEE KKK
3030Chains EEE MMM
3131Chains EEE OOO
3232Chains FFF HHH
3333Chains FFF JJJ
3434Chains FFF LLL
3535Chains FFF NNN
3636Chains FFF PPP
3737Chains GGG III
3838Chains GGG KKK
3939Chains GGG MMM
4040Chains GGG OOO
4141Chains HHH JJJ
4242Chains HHH LLL
4343Chains HHH NNN
4444Chains HHH PPP
4545Chains III KKK
4646Chains III MMM
4747Chains III OOO
4848Chains JJJ LLL
4949Chains JJJ NNN
5050Chains JJJ PPP
5151Chains KKK MMM
5252Chains KKK OOO
5353Chains LLL NNN
5454Chains LLL PPP
5555Chains MMM OOO
5656Chains NNN PPP

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56

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Components

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Protein , 2 types, 16 molecules AAACCCEEEGGGIIIKKKMMMOOOBBBDDDFFFHHHJJJLLLNNNPPP

#1: Protein
Alpha subunit of cyanobacterial protein phycoerythrin


Mass: 17572.828 Da / Num. of mol.: 8 / Source method: isolated from a natural source
Details: There are two phycoerythrobilin chromophore molecules (called PEB) in the alpha subunit of phycoerythrin. They are covalently bound to residues Cys82 (PEB166) and Cys139 (PEB167) of the ...Details: There are two phycoerythrobilin chromophore molecules (called PEB) in the alpha subunit of phycoerythrin. They are covalently bound to residues Cys82 (PEB166) and Cys139 (PEB167) of the alpha subunit, respectively.
Source: (natural) Nostoc sp. WR13 (bacteria)
Plasmid details: From the desert Rann of Kachchh (RoK), Gujarat, India
#2: Protein
Beta subunit of cyanobacterial protein phycoerythrin


Mass: 19270.975 Da / Num. of mol.: 8 / Source method: isolated from a natural source
Details: There are three phycoerythrobilin chromophore molecules (called PEB) in the beta subunit of phycoerythrin. They are covalently bound to residues Cys80 (PEB186), Cys165 (PEB187) and ...Details: There are three phycoerythrobilin chromophore molecules (called PEB) in the beta subunit of phycoerythrin. They are covalently bound to residues Cys80 (PEB186), Cys165 (PEB187) and Cys48/Cys59 (PEB188) of the beta subunit.
Source: (natural) Nostoc sp. WR13 (bacteria)
Plasmid details: From the desert Rann of Kachchh (RoK), Gujarat, India

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Non-polymers , 14 types, 1685 molecules

#3: Chemical...
ChemComp-PEB / PHYCOERYTHROBILIN


Mass: 588.694 Da / Num. of mol.: 40 / Source method: obtained synthetically / Formula: C33H40N4O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical...
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 34 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical...
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 57 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical...
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 79 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical...
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 49 / Source method: obtained synthetically / Formula: PO4
#8: Chemical...
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: NO3
#9: Chemical ChemComp-RWB / dodecaethylene glycol monomethyl ether / PEG-MME fragment n=12;polyethylene glycol monomethyl ether fragment n=12;PEG 550 MME


Mass: 560.673 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H52O13
#10: Chemical ChemComp-PE8 / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL


Mass: 370.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O9
#11: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#12: Chemical
ChemComp-P33 / 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL / HEPTAETHYLENE GLYCOL / PEG330


Mass: 326.383 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C14H30O8 / Comment: precipitant*YM
#13: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#14: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#15: Chemical ChemComp-PE5 / 3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL / 2-(2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL / POLYETHYLENE GLYCOL PEG400


Mass: 398.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38O9 / Comment: precipitant*YM
#16: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1365 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.94 Å3/Da / Density % sol: 58.09 % / Description: Rhombic Pink colour
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop
Details: Morpheus screen condition C9: 10% w/v PEG 20 000, 20% v/v PEG MME 550 precipitants; 0.03 M NPS (Nitrate, Phosphate & Sulfate) mix of additives; 0.01 M bicine/Trizma base pH 8.5 buffer system

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.13→159.07 Å / Num. obs: 156067 / % possible obs: 95.6 % / Redundancy: 10.2 % / Biso Wilson estimate: 29.7 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.283 / Rpim(I) all: 0.093 / Rrim(I) all: 0.298 / Net I/σ(I): 8
Reflection shellResolution: 2.133→2.322 Å / Redundancy: 9.3 % / Rmerge(I) obs: 1.653 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 7805 / CC1/2: 0.622 / Rpim(I) all: 0.567 / Rrim(I) all: 1.749 / % possible all: 80.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSJan 26, 2018 BUILT=20180808data processing
pointless1.11.14data scaling
Aimless0.7.2data scaling
STARANISO1.10.15 (3-May-2018)data scaling
PHASER2.8.2phasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NB4

5nb4


Resolution: 2.131→49.005 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.92 / WRfactor Rfree: 0.208 / WRfactor Rwork: 0.167 / SU B: 13.226 / SU ML: 0.164 / Average fsc free: 0.9071 / Average fsc work: 0.9199 / Cross valid method: FREE R-VALUE / ESU R: 0.335 / ESU R Free: 0.227
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.225 7765 4.976 %
Rwork0.1774 148297 -
all0.18 --
obs-156062 75.005 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 40.685 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å2-0.045 Å20 Å2
2---0.09 Å20 Å2
3---0.291 Å2
Refinement stepCycle: LAST / Resolution: 2.131→49.005 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20592 0 4153 1365 26110
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01325336
X-RAY DIFFRACTIONr_bond_other_d0.0010.01724435
X-RAY DIFFRACTIONr_angle_refined_deg1.5761.67533694
X-RAY DIFFRACTIONr_angle_other_deg1.3451.61256403
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3352910
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.41218.6411317
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.236153499
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg9.2121548
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.32315208
X-RAY DIFFRACTIONr_chiral_restr0.0770.23083
X-RAY DIFFRACTIONr_chiral_restr_other0.0530.250
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0227615
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024897
X-RAY DIFFRACTIONr_nbd_refined0.2120.25643
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1840.222926
X-RAY DIFFRACTIONr_nbtor_refined0.1590.211487
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.090.210555
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.21270
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0190.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1710.2109
X-RAY DIFFRACTIONr_nbd_other0.210.2608
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1610.284
X-RAY DIFFRACTIONr_mcbond_it2.1193.71711288
X-RAY DIFFRACTIONr_mcbond_other2.1123.71611287
X-RAY DIFFRACTIONr_mcangle_it3.1235.56814119
X-RAY DIFFRACTIONr_mcangle_other3.1255.56914120
X-RAY DIFFRACTIONr_scbond_it2.6394.07414048
X-RAY DIFFRACTIONr_scbond_other2.6394.07514034
X-RAY DIFFRACTIONr_scangle_it4.0645.97919506
X-RAY DIFFRACTIONr_scangle_other4.0665.97919486
X-RAY DIFFRACTIONr_lrange_it6.05645.82326978
X-RAY DIFFRACTIONr_lrange_other6.01345.68426797
X-RAY DIFFRACTIONr_ncsr_local_group_10.0350.055297
X-RAY DIFFRACTIONr_ncsr_local_group_20.0290.055309
X-RAY DIFFRACTIONr_ncsr_local_group_30.0340.055305
X-RAY DIFFRACTIONr_ncsr_local_group_40.0290.055316
X-RAY DIFFRACTIONr_ncsr_local_group_50.0360.055280
X-RAY DIFFRACTIONr_ncsr_local_group_60.0350.055291
X-RAY DIFFRACTIONr_ncsr_local_group_70.0620.055194
X-RAY DIFFRACTIONr_ncsr_local_group_80.0360.055696
X-RAY DIFFRACTIONr_ncsr_local_group_90.0380.055709
X-RAY DIFFRACTIONr_ncsr_local_group_100.0450.055698
X-RAY DIFFRACTIONr_ncsr_local_group_110.0360.055705
X-RAY DIFFRACTIONr_ncsr_local_group_120.0390.055700
X-RAY DIFFRACTIONr_ncsr_local_group_130.0450.055688
X-RAY DIFFRACTIONr_ncsr_local_group_140.050.055681
X-RAY DIFFRACTIONr_ncsr_local_group_150.0330.055288
X-RAY DIFFRACTIONr_ncsr_local_group_160.0380.055278
X-RAY DIFFRACTIONr_ncsr_local_group_170.0350.055285
X-RAY DIFFRACTIONr_ncsr_local_group_180.0370.055262
X-RAY DIFFRACTIONr_ncsr_local_group_190.0330.055277
X-RAY DIFFRACTIONr_ncsr_local_group_200.0610.055184
X-RAY DIFFRACTIONr_ncsr_local_group_210.0450.055728
X-RAY DIFFRACTIONr_ncsr_local_group_220.0480.055712
X-RAY DIFFRACTIONr_ncsr_local_group_230.0450.055723
X-RAY DIFFRACTIONr_ncsr_local_group_240.0450.055721
X-RAY DIFFRACTIONr_ncsr_local_group_250.0530.055708
X-RAY DIFFRACTIONr_ncsr_local_group_260.0490.055712
X-RAY DIFFRACTIONr_ncsr_local_group_270.0350.055281
X-RAY DIFFRACTIONr_ncsr_local_group_280.0310.055301
X-RAY DIFFRACTIONr_ncsr_local_group_290.0350.055270
X-RAY DIFFRACTIONr_ncsr_local_group_300.0350.055282
X-RAY DIFFRACTIONr_ncsr_local_group_310.060.055179
X-RAY DIFFRACTIONr_ncsr_local_group_320.0380.055686
X-RAY DIFFRACTIONr_ncsr_local_group_330.0380.055687
X-RAY DIFFRACTIONr_ncsr_local_group_340.0310.055695
X-RAY DIFFRACTIONr_ncsr_local_group_350.0410.055677
X-RAY DIFFRACTIONr_ncsr_local_group_360.0470.055669
X-RAY DIFFRACTIONr_ncsr_local_group_370.0250.055289
X-RAY DIFFRACTIONr_ncsr_local_group_380.0350.055254
X-RAY DIFFRACTIONr_ncsr_local_group_390.0360.055258
X-RAY DIFFRACTIONr_ncsr_local_group_400.0610.055162
X-RAY DIFFRACTIONr_ncsr_local_group_410.050.055685
X-RAY DIFFRACTIONr_ncsr_local_group_420.0470.055689
X-RAY DIFFRACTIONr_ncsr_local_group_430.0480.055683
X-RAY DIFFRACTIONr_ncsr_local_group_440.0530.055669
X-RAY DIFFRACTIONr_ncsr_local_group_450.0310.055261
X-RAY DIFFRACTIONr_ncsr_local_group_460.030.055260
X-RAY DIFFRACTIONr_ncsr_local_group_470.0590.055168
X-RAY DIFFRACTIONr_ncsr_local_group_480.0440.055713
X-RAY DIFFRACTIONr_ncsr_local_group_490.050.055702
X-RAY DIFFRACTIONr_ncsr_local_group_500.0530.055684
X-RAY DIFFRACTIONr_ncsr_local_group_510.0390.055227
X-RAY DIFFRACTIONr_ncsr_local_group_520.0620.055142
X-RAY DIFFRACTIONr_ncsr_local_group_530.0490.055701
X-RAY DIFFRACTIONr_ncsr_local_group_540.0530.055681
X-RAY DIFFRACTIONr_ncsr_local_group_550.0610.055151
X-RAY DIFFRACTIONr_ncsr_local_group_560.0550.055621
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.131-2.1860.286610.31610140.314152820.830.8317.03440.319
2.186-2.2460.3061090.27822530.28148840.8270.82815.86940.279
2.246-2.3110.2891860.25734570.259144110.830.84425.27930.254
2.311-2.3820.2862260.2449220.242141280.8430.85536.43830.234
2.382-2.460.3014350.24283870.244135850.8190.84264.93930.235
2.46-2.5460.2756250.233118500.235131960.8540.86294.53620.221
2.546-2.6420.2616040.218121460.22127530.8670.88699.97650.202
2.642-2.7490.2466620.199115850.202122470.8890.9081000.18
2.749-2.8710.2495710.192112360.194118070.90.9141000.173
2.871-3.0110.2415860.173107060.176112920.9160.9341000.15
3.011-3.1730.2375180.161101920.165107110.9220.94699.99070.141
3.173-3.3650.2095180.15196470.154101650.9450.9561000.13
3.365-3.5960.194550.13991270.14295820.9540.9641000.123
3.596-3.8820.1854330.1384930.13389260.9590.971000.116
3.882-4.250.1854220.13477920.13682140.9580.9691000.123
4.25-4.7470.1733750.12871170.13174930.9650.97499.98670.121
4.747-5.4730.1793430.14662970.14866410.9620.96999.98490.137
5.473-6.6820.2312790.19953660.256450.9410.9441000.182
6.682-9.3630.2392230.23442160.23444430.9430.94599.910.233
9.363-49.0050.361350.33724960.33826410.8870.89499.62140.375
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3866-0.1257-0.0110.0468-0.01130.19020.0094-0.0080.0051-0.0060.0081-0.0078-0.0476-0.0165-0.01760.06950.00260.0260.0120.00140.0201-2.2951150.046193.8199
20.0576-0.0809-0.03970.199-0.00320.07460.0166-0.0086-0.01270.0068-0.00770.0321-0.03210.0332-0.00890.0443-0.01350.01210.0493-0.01230.021125.5784128.7858104.5703
30.0568-0.05110.05790.0627-0.01660.19470.00720.0031-0.0167-0.00080.00170.0226-0.01570.0718-0.00890.0241-0.02660.00280.0795-0.01310.01238.227119.8717136.2864
40.1296-0.03570.02690.0104-0.00360.14210.00370.0199-0.0367-0.0052-0.00830.0084-0.04960.01750.00470.0558-0.01050.0110.04240.00190.021410.4415140.2018125.1872
50.4346-0.2484-0.15540.19750.0580.2318-0.02050.00730.01540.00440.034-0.0065-0.06210.0035-0.01350.0627-0.0194-0.00030.0310.00060.00177.569149.5942148.901
60.0548-0.0675-0.02190.2433-0.07210.0883-0.0091-0.0157-0.00810.03770.01880.0267-0.0240.0425-0.00970.0335-0.0188-0.00160.0753-0.00440.007228.8727122.0441159.9561
70.028-0.0865-0.01020.34580.09920.23920.009-0.0105-0.002-0.0102-0.00940.01160.01740.06810.00040.0095-0.011-0.0040.08650.0020.015938.9302109.9418191.1506
80.1429-0.08230.05640.0546-0.00660.1241-0.0020.0222-0.0173-0.0156-0.00590.0129-0.05030.03540.0080.0528-0.0133-0.00550.0428-0.00120.015917.2674137.1995180.322
90.3696-0.2964-0.04080.25190.02450.1457-0.0104-0.0133-0.0005-0.00560.01920.0084-0.06360.0435-0.00880.0534-0.0321-0.00880.0229-0.00160.024217.0733146.3294203.9902
100.00190.01220.0140.24810.03490.17780.00180.00160.0010.0209-0.01140.0673-0.00220.08160.00960.0048-0.01290.00090.07190.01210.043830.7837113.9908214.7413
110.0249-0.01570.07450.53370.09540.27460.0060.00910.00020.02420.0113-0.0090.03790.0515-0.01730.01110.0154-0.01530.04970.00520.05937.6226100.3788246.3846
120.2679-0.16790.09290.1462-0.06560.104800.0531-0.001-0.0061-0.03850.0169-0.03880.04870.03860.026-0.0191-0.01890.049-0.00020.049522.7726132.5809235.4178
130.3096-0.08350.16550.0501-0.05650.126-0.01530.0280.03560.0296-0.03440.0107-0.04330.03880.04970.0417-0.0355-0.01180.0343-0.00250.065724.8165141.0184259.0182
140.08740.1743-0.07950.3601-0.13170.17610.0139-0.01450.01050.0267-0.01610.04490.00560.06590.00220.01380.004-0.01940.04820.00050.078330.6921106.7575270.0364
150.23850.21120.04731.3005-0.40050.21490.0263-0.1261-0.08280.1433-0.0169-0.11020-0.0368-0.00940.07550.033-0.02330.09780.03450.031734.211991.4617301.2189
160.2327-0.40150.05230.767-0.02460.1134-0.00060.0190.01640.0399-0.0305-0.0347-0.00580.0160.03110.0543-0.0031-0.03610.0247-0.00640.037227.1332125.7127290.5942
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAAA1 - 999
2X-RAY DIFFRACTION2ALLBBB1 - 999
3X-RAY DIFFRACTION3ALLCCC1 - 999
4X-RAY DIFFRACTION4ALLDDD1 - 999
5X-RAY DIFFRACTION5ALLEEE1 - 999
6X-RAY DIFFRACTION6ALLFFF1 - 999
7X-RAY DIFFRACTION7ALLGGG1 - 999
8X-RAY DIFFRACTION8ALLHHH1 - 999
9X-RAY DIFFRACTION9ALLIII1 - 999
10X-RAY DIFFRACTION10ALLJJJ1 - 999
11X-RAY DIFFRACTION11ALLKKK1 - 999
12X-RAY DIFFRACTION12ALLLLL1 - 999
13X-RAY DIFFRACTION13ALLMMM1 - 999
14X-RAY DIFFRACTION14ALLNNN1 - 999
15X-RAY DIFFRACTION15ALLOOO1 - 999
16X-RAY DIFFRACTION16ALLPPP1 - 999

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