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- PDB-3oda: Human PARP-1 zinc finger 1 (Zn1) bound to DNA -

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Basic information

Entry
Database: PDB / ID: 3oda
TitleHuman PARP-1 zinc finger 1 (Zn1) bound to DNA
Components
  • 5'-D(*GP*CP*CP*TP*GP*CP*AP*GP*GP*C)-3'
  • Poly [ADP-ribose] polymerase 1
KeywordsDNA BINDING PROTEIN/DNA / protein-DNA complex / PARP zinc finger / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


NAD+-histone H2BS6 serine ADP-ribosyltransferase activity / NAD+-histone H3S10 serine ADP-ribosyltransferase activity / NAD+-histone H2BE35 glutamate ADP-ribosyltransferase activity / regulation of base-excision repair / positive regulation of myofibroblast differentiation / negative regulation of ATP biosynthetic process / NAD+-protein-tyrosine ADP-ribosyltransferase activity / NAD+-protein-histidine ADP-ribosyltransferase activity / carbohydrate biosynthetic process / regulation of circadian sleep/wake cycle, non-REM sleep ...NAD+-histone H2BS6 serine ADP-ribosyltransferase activity / NAD+-histone H3S10 serine ADP-ribosyltransferase activity / NAD+-histone H2BE35 glutamate ADP-ribosyltransferase activity / regulation of base-excision repair / positive regulation of myofibroblast differentiation / negative regulation of ATP biosynthetic process / NAD+-protein-tyrosine ADP-ribosyltransferase activity / NAD+-protein-histidine ADP-ribosyltransferase activity / carbohydrate biosynthetic process / regulation of circadian sleep/wake cycle, non-REM sleep / positive regulation of single strand break repair / vRNA Synthesis / negative regulation of adipose tissue development / NAD+-protein-serine ADP-ribosyltransferase activity / NAD DNA ADP-ribosyltransferase activity / NAD+- protein-aspartate ADP-ribosyltransferase activity / NAD+-protein-glutamate ADP-ribosyltransferase activity / mitochondrial DNA metabolic process / DNA ADP-ribosylation / regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / signal transduction involved in regulation of gene expression / positive regulation of necroptotic process / regulation of catalytic activity / ATP generation from poly-ADP-D-ribose / replication fork reversal / transcription regulator activator activity / HDR through MMEJ (alt-NHEJ) / positive regulation of DNA-templated transcription, elongation / positive regulation of intracellular estrogen receptor signaling pathway / NAD+ ADP-ribosyltransferase / cellular response to zinc ion / negative regulation of telomere maintenance via telomere lengthening / protein auto-ADP-ribosylation / positive regulation of mitochondrial depolarization / response to aldosterone / mitochondrial DNA repair / negative regulation of cGAS/STING signaling pathway / protein poly-ADP-ribosylation / positive regulation of cardiac muscle hypertrophy / negative regulation of transcription elongation by RNA polymerase II / nuclear replication fork / NAD+-protein ADP-ribosyltransferase activity / R-SMAD binding / site of DNA damage / positive regulation of SMAD protein signal transduction / protein autoprocessing / macrophage differentiation / decidualization / Transferases; Glycosyltransferases; Pentosyltransferases / positive regulation of double-strand break repair via homologous recombination / NAD+ ADP-ribosyltransferase activity / POLB-Dependent Long Patch Base Excision Repair / SUMOylation of DNA damage response and repair proteins / nucleosome binding / protein localization to chromatin / negative regulation of innate immune response / telomere maintenance / nucleotidyltransferase activity / mitochondrion organization / transforming growth factor beta receptor signaling pathway / cellular response to nerve growth factor stimulus / nuclear estrogen receptor binding / response to gamma radiation / protein-DNA complex / Downregulation of SMAD2/3:SMAD4 transcriptional activity / DNA Damage Recognition in GG-NER / protein modification process / Dual Incision in GG-NER / Formation of Incision Complex in GG-NER / histone deacetylase binding / positive regulation of protein localization to nucleus / cellular response to amyloid-beta / cellular response to insulin stimulus / regulation of protein localization / cellular response to UV / NAD binding / double-strand break repair / nuclear envelope / site of double-strand break / cellular response to oxidative stress / positive regulation of canonical NF-kappaB signal transduction / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / transcription by RNA polymerase II / chromosome, telomeric region / damaged DNA binding / nuclear body / DNA repair / innate immune response / negative regulation of DNA-templated transcription / apoptotic process / ubiquitin protein ligase binding / DNA damage response / chromatin binding / chromatin / nucleolus / protein kinase binding / enzyme binding / negative regulation of transcription by RNA polymerase II / protein homodimerization activity
Similarity search - Function
Zinc finger, PARP-type / first zn-finger domain of poly(adp-ribose) polymerase-1 / : / PADR1, N-terminal helical domain / PADR1 domain profile. / Poly [ADP-ribose] polymerase / PADR1 domain / PADR1 domain superfamily / PADR1 domain, zinc ribbon fold / PADR1 ...Zinc finger, PARP-type / first zn-finger domain of poly(adp-ribose) polymerase-1 / : / PADR1, N-terminal helical domain / PADR1 domain profile. / Poly [ADP-ribose] polymerase / PADR1 domain / PADR1 domain superfamily / PADR1 domain, zinc ribbon fold / PADR1 / Zinc finger poly(ADP-ribose) polymerase (PARP)-type signature. / Zinc finger, PARP-type superfamily / Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region / Zinc finger poly(ADP-ribose) polymerase (PARP)-type profile. / Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region / Zinc finger, PARP-type / WGR domain profile. / Poly(ADP-ribose) polymerase, regulatory domain / WGR domain / WGR domain superfamily / WGR domain / Proposed nucleic acid binding domain / Poly(ADP-ribose) polymerase, regulatory domain superfamily / Poly(ADP-ribose) polymerase, regulatory domain / PARP alpha-helical domain profile. / BRCA1 C Terminus (BRCT) domain / Poly(ADP-ribose) polymerase catalytic domain / Poly(ADP-ribose) polymerase, catalytic domain / PARP catalytic domain profile. / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / Poly [ADP-ribose] polymerase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 Å
AuthorsPascal, J.M. / Langelier, M.-F.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Crystal Structures of Poly(ADP-ribose) Polymerase-1 (PARP-1) Zinc Fingers Bound to DNA: STRUCTURAL AND FUNCTIONAL INSIGHTS INTO DNA-DEPENDENT PARP-1 ACTIVITY.
Authors: Langelier, M.F. / Planck, J.L. / Roy, S. / Pascal, J.M.
History
DepositionAug 11, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Poly [ADP-ribose] polymerase 1
B: Poly [ADP-ribose] polymerase 1
C: Poly [ADP-ribose] polymerase 1
D: Poly [ADP-ribose] polymerase 1
E: Poly [ADP-ribose] polymerase 1
F: Poly [ADP-ribose] polymerase 1
G: Poly [ADP-ribose] polymerase 1
H: Poly [ADP-ribose] polymerase 1
I: 5'-D(*GP*CP*CP*TP*GP*CP*AP*GP*GP*C)-3'
J: 5'-D(*GP*CP*CP*TP*GP*CP*AP*GP*GP*C)-3'
K: 5'-D(*GP*CP*CP*TP*GP*CP*AP*GP*GP*C)-3'
L: 5'-D(*GP*CP*CP*TP*GP*CP*AP*GP*GP*C)-3'
M: 5'-D(*GP*CP*CP*TP*GP*CP*AP*GP*GP*C)-3'
N: 5'-D(*GP*CP*CP*TP*GP*CP*AP*GP*GP*C)-3'
O: 5'-D(*GP*CP*CP*TP*GP*CP*AP*GP*GP*C)-3'
P: 5'-D(*GP*CP*CP*TP*GP*CP*AP*GP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,70624
Polymers129,18316
Non-polymers5238
Water4,197233
1
A: Poly [ADP-ribose] polymerase 1
B: Poly [ADP-ribose] polymerase 1
I: 5'-D(*GP*CP*CP*TP*GP*CP*AP*GP*GP*C)-3'
J: 5'-D(*GP*CP*CP*TP*GP*CP*AP*GP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4266
Polymers32,2964
Non-polymers1312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Poly [ADP-ribose] polymerase 1
D: Poly [ADP-ribose] polymerase 1
K: 5'-D(*GP*CP*CP*TP*GP*CP*AP*GP*GP*C)-3'
L: 5'-D(*GP*CP*CP*TP*GP*CP*AP*GP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4266
Polymers32,2964
Non-polymers1312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Poly [ADP-ribose] polymerase 1
F: Poly [ADP-ribose] polymerase 1
M: 5'-D(*GP*CP*CP*TP*GP*CP*AP*GP*GP*C)-3'
N: 5'-D(*GP*CP*CP*TP*GP*CP*AP*GP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4266
Polymers32,2964
Non-polymers1312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Poly [ADP-ribose] polymerase 1
H: Poly [ADP-ribose] polymerase 1
O: 5'-D(*GP*CP*CP*TP*GP*CP*AP*GP*GP*C)-3'
P: 5'-D(*GP*CP*CP*TP*GP*CP*AP*GP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4266
Polymers32,2964
Non-polymers1312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.812, 107.334, 86.998
Angle α, β, γ (deg.)90.000, 100.610, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
31E
41G
12B
22D
32F
42H
13B
23A
33D
43F
53H
14C
24E
34G

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain 'A' and (resseq 7:9 or resseq 11:38 or resseq...A0
211chain 'C' and (resseq 7:9 or resseq 11:38 or resseq...C0
311chain 'E' and (resseq 7:9 or resseq 11:38 or resseq...E0
411chain 'G' and (resseq 7:9 or resseq 11:38 or resseq...G0
112chain 'B' and (resseq 7:9 or resseq 11:38 or resseq...B0
212chain 'D' and (resseq 7:9 or resseq 11:38 or resseq...D0
312chain 'F' and (resseq 7:9 or resseq 11:38 or resseq...F0
412chain 'H' and (resseq 7:9 or resseq 11:38 or resseq...H0
113chain 'B' and (resseq 39:47) and (not element H) and (not element D) and backboneB0
213chain 'A' and (resseq 39:47) and (not element H) and (not element D) and backboneA0
313chain 'D' and (resseq 39:47) and (not element H) and (not element D) and backboneD0
413chain 'F' and (resseq 39:47) and (not element H) and (not element D) and backboneF0
513chain 'H' and (resseq 39:47) and (not element H) and (not element D) and backboneH0
114chain 'C' and (resseq 39:47) and (not element H) and (not element D) and backboneC0
214chain 'E' and (resseq 39:47) and (not element H) and (not element D) and backboneE0
314chain 'G' and (resseq 39:47) and (not element H) and (not element D) and backboneG0

NCS ensembles :
ID
1
2
3
4

NCS oper:
IDCodeMatrixVector
1given(0.991952, 0.042233, 0.119362), (0.05383, -0.993957, -0.095665), (0.1146, 0.101321, -0.988231)21.921301, 93.544998, 76.982803
2given(0.990774, -0.016573, 0.134504), (-0.00112, -0.993461, -0.114164), (0.135516, 0.11296, -0.984315)-1.87424, 88.976196, 115.935997
3given(0.998634, -0.019534, -0.04846), (0.020387, 0.999645, 0.01716), (0.048107, -0.018124, 0.998678)45.682701, -11.5554, -40.965801
4given(0.992906, -0.006149, 0.118743), (-0.020396, -0.992668, 0.119137), (0.11714, -0.120713, -0.985752)26.9881, 84.348701, 90.0224
5given(0.987538, 0.035505, 0.153321), (0.013307, -0.989569, 0.143446), (0.156815, -0.139618, -0.97771)-6.26136, 67.205399, 127.366997
6given(0.998995, -0.01284, -0.042939), (0.012574, 0.9999, -0.006471), (0.043017, 0.005925, 0.999057)41.994801, -9.41443, -43.106602
7given(-0.683511, -0.095243, 0.7237), (0.356998, -0.908401, 0.217623), (0.636683, 0.407107, 0.654903)9.09951, 43.797001, -10.9409
8given(0.995769, -0.008054, 0.091537), (-0.018791, -0.992949, 0.117045), (0.089949, -0.11827, -0.988899)28.483299, 84.285004, 90.012001
9given(0.992458, 0.026306, 0.11973), (0.008147, -0.988698, 0.149697), (0.122314, -0.147592, -0.981456)-3.00526, 66.6185, 128.671997
10given(0.998884, -0.03034, -0.036193), (0.027916, 0.997449, -0.065701), (0.038094, 0.064617, 0.997183)42.525902, -4.50145, -46.699001
11given(0.998226, -0.058976, -0.008158), (0.059068, 0.998186, 0.011619), (0.007458, -0.01208, 0.999899)-17.4291, 8.06851, -41.615601
12given(0.96618, 0.101086, 0.237228), (0.077696, -0.991329, 0.105976), (0.245883, -0.08396, -0.965656)-12.9245, 92.2658, 130.367004

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Components

#1: Protein
Poly [ADP-ribose] polymerase 1 / PARP-1 / NAD(+) ADP-ribosyltransferase 1 / ADPRT 1 / Poly[ADP-ribose] synthase 1


Mass: 13101.821 Da / Num. of mol.: 8 / Fragment: PARP-1 zinc finger 1, Zn1, UNP residues 2-96
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADPRT, PARP1, PPOL / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Rosetta2 / References: UniProt: P09874, NAD+ ADP-ribosyltransferase
#2: DNA chain
5'-D(*GP*CP*CP*TP*GP*CP*AP*GP*GP*C)-3'


Mass: 3045.992 Da / Num. of mol.: 8 / Source method: obtained synthetically / Details: Chemically synthesized DNA
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / Source method: isolated from a natural source / Formula: H2O

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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: 2.23 Å3/Da / Density % sol: 44.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8.5
Details: 30% PEG 3350, 100 mM NaAcetate, 100 mM Tris pH 8.5, 0.1 mM TCEP, 20% ethylene glycol, vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.99 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Sep 18, 2009
RadiationMonochromator: silicon(111) crystal / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 2.64→50 Å / Num. obs: 33279 / % possible obs: 99.9 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.09 / Χ2: 0.997 / Net I/σ(I): 9.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.64-2.74.30.50916431.037199.9
2.7-2.744.20.516571.0451100
2.74-2.84.30.42516630.9921100
2.8-2.854.20.36416491.0371100
2.85-2.924.20.31116610.9861100
2.92-2.984.30.27716700.972199.9
2.98-3.064.30.2316320.9551100
3.06-3.144.30.18316731.0361100
3.14-3.234.20.12416561.0141100
3.23-3.344.20.09616621.012199.9
3.34-3.464.20.08216720.985199.9
3.46-3.64.30.07916431.0031100
3.6-3.764.20.06516771.0351100
3.76-3.964.20.05716710.972199.9
3.96-4.214.20.05116480.966199.9
4.21-4.534.20.04916610.964199.9
4.53-4.994.20.04916700.976199.9
4.99-5.714.20.04816851.0071100
5.71-7.194.20.05716770.974199.9
7.19-5040.03817090.962199.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.6.1_357refinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.64→42.42 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8008 / SU ML: 0.36 / σ(F): 1.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2455 1677 5.05 %
Rwork0.1963 --
obs0.1989 33211 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.345 Å2 / ksol: 0.334 e/Å3
Displacement parametersBiso max: 103.21 Å2 / Biso mean: 35.0196 Å2 / Biso min: 10.11 Å2
Baniso -1Baniso -2Baniso -3
1-8.3484 Å2-0 Å22.1462 Å2
2---9.9649 Å2-0 Å2
3---1.6165 Å2
Refinement stepCycle: LAST / Resolution: 2.64→42.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5695 1616 8 233 7552
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0117731
X-RAY DIFFRACTIONf_angle_d1.28810687
X-RAY DIFFRACTIONf_chiral_restr0.0721092
X-RAY DIFFRACTIONf_plane_restr0.0051084
X-RAY DIFFRACTIONf_dihedral_angle_d21.8812991
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A556X-RAY DIFFRACTIONPOSITIONAL0.04
12C556X-RAY DIFFRACTIONPOSITIONAL0.04
13E557X-RAY DIFFRACTIONPOSITIONAL0.051
14G548X-RAY DIFFRACTIONPOSITIONAL0.046
21B551X-RAY DIFFRACTIONPOSITIONAL0.051
22D551X-RAY DIFFRACTIONPOSITIONAL0.051
23F552X-RAY DIFFRACTIONPOSITIONAL0.055
24H552X-RAY DIFFRACTIONPOSITIONAL0.052
31B36X-RAY DIFFRACTIONPOSITIONAL0.264
32A36X-RAY DIFFRACTIONPOSITIONAL0.264
33D36X-RAY DIFFRACTIONPOSITIONAL0.182
34F36X-RAY DIFFRACTIONPOSITIONAL0.245
35H36X-RAY DIFFRACTIONPOSITIONAL0.186
41C36X-RAY DIFFRACTIONPOSITIONAL0.253
42E36X-RAY DIFFRACTIONPOSITIONAL0.253
43G36X-RAY DIFFRACTIONPOSITIONAL0.199
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6411-2.73540.32711400.25563084322497
2.7354-2.84490.30291560.251431613317100
2.8449-2.97440.35231740.242431593333100
2.9744-3.13120.27981870.229531273314100
3.1312-3.32730.26691600.19813145330599
3.3273-3.5840.26751650.19231543319100
3.584-3.94450.24321640.18231803344100
3.9445-4.51470.22191760.161631473323100
4.5147-5.68590.18171680.151731943362100
5.6859-42.42670.17641870.16343183337099

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  • 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

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