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- PDB-7fbj: Crystal structure of SARS-CoV-2 receptor binding domain in comple... -

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Basic information

Entry
Database: PDB / ID: 7fbj
TitleCrystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing nanobody 17F6
Components
  • New antigen receptor variable domain
  • Spike protein S1
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / SARS-CoV-2 / Spike glycoprotein / RBD / VNAR / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / membrane / identical protein binding / plasma membrane
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus 2
Chiloscyllium plagiosum (whitespotted bambooshark)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsZhu, J. / Xu, T. / Feng, B. / Liu, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Small Methods / Year: 2022
Title: A Class of Shark-Derived Single-Domain Antibodies can Broadly Neutralize SARS-Related Coronaviruses and the Structural Basis of Neutralization and Omicron Escape.
Authors: Feng, B. / Chen, Z. / Sun, J. / Xu, T. / Wang, Q. / Yi, H. / Niu, X. / Zhu, J. / Fan, M. / Hou, R. / Shao, Y. / Huang, S. / Li, C. / Hu, P. / Zheng, P. / He, P. / Luo, J. / Yan, Q. / Xiong, ...Authors: Feng, B. / Chen, Z. / Sun, J. / Xu, T. / Wang, Q. / Yi, H. / Niu, X. / Zhu, J. / Fan, M. / Hou, R. / Shao, Y. / Huang, S. / Li, C. / Hu, P. / Zheng, P. / He, P. / Luo, J. / Yan, Q. / Xiong, X. / Liu, J. / Zhao, J. / Chen, L.
History
DepositionJul 11, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 13, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Spike protein S1
B: New antigen receptor variable domain
C: Spike protein S1
D: New antigen receptor variable domain
E: Spike protein S1
F: New antigen receptor variable domain
G: Spike protein S1
H: New antigen receptor variable domain
I: Spike protein S1
J: New antigen receptor variable domain
K: Spike protein S1
L: New antigen receptor variable domain
M: Spike protein S1
N: New antigen receptor variable domain
O: Spike protein S1
P: New antigen receptor variable domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)319,07524
Polymers316,12816
Non-polymers2,9488
Water21612
1
A: Spike protein S1
B: New antigen receptor variable domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7373
Polymers39,5162
Non-polymers2211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Spike protein S1
D: New antigen receptor variable domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7373
Polymers39,5162
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Spike protein S1
F: New antigen receptor variable domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7373
Polymers39,5162
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Spike protein S1
H: New antigen receptor variable domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9403
Polymers39,5162
Non-polymers4241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
I: Spike protein S1
J: New antigen receptor variable domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9403
Polymers39,5162
Non-polymers4241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
K: Spike protein S1
L: New antigen receptor variable domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1023
Polymers39,5162
Non-polymers5871
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
M: Spike protein S1
N: New antigen receptor variable domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9403
Polymers39,5162
Non-polymers4241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
O: Spike protein S1
P: New antigen receptor variable domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9403
Polymers39,5162
Non-polymers4241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.020, 73.753, 270.717
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22E
13A
23G
14A
24I
15A
25K
16A
26M
17A
27O
18B
28D
19B
29F
110B
210H
111B
211J
112B
212L
113B
213N
114B
214P
115C
215E
116C
216G
117C
217I
118C
218K
119C
219M
120C
220O
121D
221F
122D
222H
123D
223J
124D
224L
125D
225N
126D
226P
127E
227G
128E
228I
129E
229K
130E
230M
131E
231O
132F
232H
133F
233J
134F
234L
135F
235N
136F
236P
137G
237I
138G
238K
139G
239M
140G
240O
141H
241J
142H
242L
143H
243N
144H
244P
145I
245K
146I
246M
147I
247O
148J
248L
149J
249N
150J
250P
151K
251M
152K
252O
153L
253N
154L
254P
155M
255O
156N
256P

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRALAALAAA333 - 5288 - 203
21THRTHRALAALACC333 - 5288 - 203
12THRTHRGLYGLYAA333 - 5268 - 201
22THRTHRGLYGLYEE333 - 5268 - 201
13THRTHRALAALAAA333 - 5298 - 204
23THRTHRALAALAGG333 - 5298 - 204
14THRTHRALAALAAA333 - 5298 - 204
24THRTHRALAALAII333 - 5298 - 204
15THRTHRALAALAAA333 - 5298 - 204
25THRTHRALAALAKK333 - 5298 - 204
16THRTHRALAALAAA333 - 5298 - 204
26THRTHRALAALAMM333 - 5298 - 204
17THRTHRALAALAAA333 - 5288 - 203
27THRTHRALAALAOO333 - 5288 - 203
18ALAALAASNASNBB0 - 1094 - 113
28ALAALAASNASNDD0 - 1094 - 113
19ALAALAASNASNBB0 - 1094 - 113
29ALAALAASNASNFF0 - 1094 - 113
110ALAALAASNASNBB0 - 1094 - 113
210ALAALAASNASNHH0 - 1094 - 113
111ALAALAASNASNBB0 - 1094 - 113
211ALAALAASNASNJJ0 - 1094 - 113
112ALAALAASNASNBB0 - 1094 - 113
212ALAALAASNASNLL0 - 1094 - 113
113ALAALAASNASNBB0 - 1094 - 113
213ALAALAASNASNNN0 - 1094 - 113
114GLUGLUASNASNBB1 - 1095 - 113
214GLUGLUASNASNPP1 - 1095 - 113
115THRTHRGLYGLYCC333 - 5268 - 201
215THRTHRGLYGLYEE333 - 5268 - 201
116THRTHRALAALACC333 - 5288 - 203
216THRTHRALAALAGG333 - 5288 - 203
117THRTHRALAALACC333 - 5288 - 203
217THRTHRALAALAII333 - 5288 - 203
118THRTHRALAALACC333 - 5288 - 203
218THRTHRALAALAKK333 - 5288 - 203
119THRTHRALAALACC333 - 5288 - 203
219THRTHRALAALAMM333 - 5288 - 203
120THRTHRALAALACC333 - 5298 - 204
220THRTHRALAALAOO333 - 5298 - 204
121ALAALASERSERDD0 - 1104 - 114
221ALAALASERSERFF0 - 1104 - 114
122ALAALASERSERDD0 - 1104 - 114
222ALAALASERSERHH0 - 1104 - 114
123ALAALASERSERDD0 - 1104 - 114
223ALAALASERSERJJ0 - 1104 - 114
124ALAALASERSERDD0 - 1114 - 115
224ALAALASERSERLL0 - 1114 - 115
125ALAALASERSERDD0 - 1104 - 114
225ALAALASERSERNN0 - 1104 - 114
126GLUGLUSERSERDD1 - 1105 - 114
226GLUGLUSERSERPP1 - 1105 - 114
127THRTHRGLYGLYEE333 - 5268 - 201
227THRTHRGLYGLYGG333 - 5268 - 201
128THRTHRGLYGLYEE333 - 5268 - 201
228THRTHRGLYGLYII333 - 5268 - 201
129THRTHRGLYGLYEE333 - 5268 - 201
229THRTHRGLYGLYKK333 - 5268 - 201
130THRTHRGLYGLYEE333 - 5268 - 201
230THRTHRGLYGLYMM333 - 5268 - 201
131THRTHRGLYGLYEE333 - 5268 - 201
231THRTHRGLYGLYOO333 - 5268 - 201
132ALAALASERSERFF0 - 1104 - 114
232ALAALASERSERHH0 - 1104 - 114
133ALAALASERSERFF0 - 1104 - 114
233ALAALASERSERJJ0 - 1104 - 114
134ALAALASERSERFF0 - 1104 - 114
234ALAALASERSERLL0 - 1104 - 114
135ALAALASERSERFF0 - 1104 - 114
235ALAALASERSERNN0 - 1104 - 114
136GLUGLUSERSERFF1 - 1105 - 114
236GLUGLUSERSERPP1 - 1105 - 114
137THRTHRALAALAGG333 - 5308 - 205
237THRTHRALAALAII333 - 5308 - 205
138THRTHRALAALAGG333 - 5308 - 205
238THRTHRALAALAKK333 - 5308 - 205
139THRTHRALAALAGG333 - 5308 - 205
239THRTHRALAALAMM333 - 5308 - 205
140THRTHRALAALAGG333 - 5288 - 203
240THRTHRALAALAOO333 - 5288 - 203
141ALAALASERSERHH-2 - 1112 - 115
241ALAALASERSERJJ-2 - 1112 - 115
142ALAALASERSERHH0 - 1104 - 114
242ALAALASERSERLL0 - 1104 - 114
143METMETSERSERHH-1 - 1103 - 114
243METMETSERSERNN-1 - 1103 - 114
144GLUGLUSERSERHH1 - 1105 - 114
244GLUGLUSERSERPP1 - 1105 - 114
145THRTHRALAALAII333 - 5308 - 205
245THRTHRALAALAKK333 - 5308 - 205
146THRTHRALAALAII333 - 5308 - 205
246THRTHRALAALAMM333 - 5308 - 205
147THRTHRALAALAII333 - 5288 - 203
247THRTHRALAALAOO333 - 5288 - 203
148ALAALASERSERJJ0 - 1104 - 114
248ALAALASERSERLL0 - 1104 - 114
149METMETSERSERJJ-1 - 1103 - 114
249METMETSERSERNN-1 - 1103 - 114
150GLUGLUSERSERJJ1 - 1105 - 114
250GLUGLUSERSERPP1 - 1105 - 114
151THRTHRALAALAKK333 - 5308 - 205
251THRTHRALAALAMM333 - 5308 - 205
152THRTHRALAALAKK333 - 5288 - 203
252THRTHRALAALAOO333 - 5288 - 203
153ALAALASERSERLL0 - 1104 - 114
253ALAALASERSERNN0 - 1104 - 114
154GLUGLUSERSERLL1 - 1105 - 114
254GLUGLUSERSERPP1 - 1105 - 114
155THRTHRALAALAMM333 - 5288 - 203
255THRTHRALAALAOO333 - 5288 - 203
156GLUGLUSERSERNN1 - 1105 - 114
256GLUGLUSERSERPP1 - 1105 - 114

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 ACEGIKMOBDFHJLNP

#1: Protein
Spike protein S1


Mass: 25623.520 Da / Num. of mol.: 8 / Fragment: receptor binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Plasmid: pSECtag2A / Cell line (production host): 293F / Production host: Homo sapiens (human) / References: UniProt: P0DTC2
#2: Protein
New antigen receptor variable domain


Mass: 13892.436 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chiloscyllium plagiosum (whitespotted bambooshark)
Production host: Escherichia coli (E. coli)

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Sugars , 3 types, 8 molecules

#3: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 1 types, 12 molecules

#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.59 Å3/Da / Density % sol: 52.51 % / Mosaicity: 0 °
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 0.22M Sodium citrate tribasic dihydrate 23% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.85→135.36 Å / Num. obs: 76077 / % possible obs: 99.8 % / Redundancy: 5.1 % / CC1/2: 0.961 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.064 / Rrim(I) all: 0.145 / Net I/σ(I): 7.2 / Num. measured all: 390964 / Scaling rejects: 4446
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.85-2.915.30.6462363344620.8770.3060.7171.899.2
14.25-135.363.80.07525306610.9290.0460.08910.796.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2i26, 7eam

2i26

7eam


Resolution: 2.85→90.4 Å / Cor.coef. Fo:Fc: 0.864 / Cor.coef. Fo:Fc free: 0.822 / SU B: 50.198 / SU ML: 0.412 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.452 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.3004 3645 4.8 %RANDOM
Rwork0.2537 ---
obs0.2559 72371 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 189.96 Å2 / Biso mean: 79.508 Å2 / Biso min: 39.86 Å2
Baniso -1Baniso -2Baniso -3
1-7.18 Å2-0 Å2-0.04 Å2
2--0.06 Å20 Å2
3----7.25 Å2
Refinement stepCycle: final / Resolution: 2.85→90.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19282 0 193 12 19487
Biso mean--119.57 59.08 -
Num. residues----2480
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01319993
X-RAY DIFFRACTIONr_bond_other_d0.0010.01417951
X-RAY DIFFRACTIONr_angle_refined_deg1.7941.66627194
X-RAY DIFFRACTIONr_angle_other_deg1.3321.59141329
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.04252464
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.20921.9531024
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.885153058
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.89915120
X-RAY DIFFRACTIONr_chiral_restr0.0880.22630
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0222923
X-RAY DIFFRACTIONr_gen_planes_other0.0030.024962
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A61500.06
12C61500.06
21A61390.05
22E61390.05
31A60870.07
32G60870.07
41A60850.07
42I60850.07
51A61170.07
52K61170.07
61A62040.06
62M62040.06
71A60850.07
72O60850.07
81B32930.04
82D32930.04
91B32840.05
92F32840.05
101B32190.06
102H32190.06
111B32150.09
112J32150.09
121B31830.07
122L31830.07
131B32940.07
132N32940.07
141B32010.06
142P32010.06
151C61640.04
152E61640.04
161C60870.06
162G60870.06
171C60830.06
172I60830.06
181C60900.06
182K60900.06
191C61860.05
192M61860.05
201C61090.06
202O61090.06
211D33420.02
212F33420.02
221D32450.06
222H32450.06
231D32420.08
232J32420.08
241D32210.07
242L32210.07
251D32680.07
252N32680.07
261D32320.06
262P32320.06
271E60910.05
272G60910.05
281E60840.05
282I60840.05
291E61110.06
292K61110.06
301E61210.05
302M61210.05
311E61190.05
312O61190.05
321F32360.06
322H32360.06
331F32350.08
332J32350.08
341F32040.07
342L32040.07
351F32790.07
352N32790.07
361F32280.06
362P32280.06
371G62710.04
372I62710.04
381G61850.05
382K61850.05
391G60640.07
392M60640.07
401G60970.06
402O60970.06
411H33510.07
412J33510.07
421H32520.06
422L32520.06
431H32250.09
432N32250.09
441H32400.05
442P32400.05
451I61790.05
452K61790.05
461I60580.07
462M60580.07
471I60880.06
472O60880.06
481J32460.07
482L32460.07
491J32490.08
492N32490.08
501J32570.06
502P32570.06
511K61150.07
512M61150.07
521K61790.05
522O61790.05
531L31700.09
532N31700.09
541L32570.03
542P32570.03
551M60790.07
552O60790.07
561N31930.08
562P31930.08
LS refinement shellResolution: 2.85→2.924 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.387 278 -
Rwork0.363 5322 -
all-5600 -
obs--99.77 %
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)
11.4114-0.6163-0.79141.16660.55271.86860.0899-0.08360.03290.17420.0594-0.09990.07150.369-0.14930.0641-0.0173-0.02610.3802-0.12130.302330.85427.6-46.63
23.79961.1973-1.27871.4039-1.07141.96830.15290.0639-0.6098-0.1655-0.14090.05330.1592-0.0232-0.01190.0848-0.0254-0.11270.2701-0.13280.370313.45812.716-59.872
32.22930.29310.49191.7180.96720.89680.2974-0.1376-0.508-0.0905-0.05070.03150.1756-0.2084-0.24670.1904-0.0879-0.24310.33260.010.360223.01517.511-115.184
42.6259-1.8545-1.42093.880.20421.19820.1110.2777-0.0667-0.18570.03120.3628-0.0867-0.4997-0.14220.35020.2335-0.26250.6245-0.0070.29367.73136.241-126.561
51.7673-0.2138-0.42591.98260.95170.96930.23220.17170.45830.0905-0.01740.0792-0.233-0.2571-0.21480.16890.1070.18490.3066-0.00110.2939-17.879-0.505-20.27
62.3651.79991.61833.40720.40811.59850.1371-0.23630.06370.15490.06870.40380.0902-0.4903-0.20570.3003-0.23470.21690.57730.01940.2807-33.343-19.24-8.843
71.76060.02061.0930.3946-0.01711.1101-0.0751-0.3385-0.28290.15640.15520.25040.2493-0.098-0.08010.30620.10420.20730.35890.16540.27022.97120.556-15.969
81.363-1.031-0.46742.25441.12691.9808-0.3009-0.43160.06640.20620.3527-0.14520.12150.0522-0.05180.09830.07310.04220.3637-0.04650.17037.09946.136-22.204
92.0723-0.1238-1.17560.5680.07841.0916-0.12890.39840.2929-0.16020.17480.2153-0.2568-0.1537-0.04590.3447-0.0965-0.23350.36320.15180.2661-38.011-3.443-119.367
101.00360.54880.4732.62310.57231.4658-0.27340.3414-0.0768-0.31570.3019-0.1396-0.11020.0672-0.02850.1448-0.0866-0.0740.4117-0.06610.1935-33.913-29.041-113.193
110.8982-0.68240.13862.5497-2.12412.1764-0.09570.008-0.102-0.44240.3630.23660.5561-0.5426-0.26730.166-0.1795-0.05930.4557-0.02450.2313-23.164-27.251-52.362
122.6911-0.8465-1.17050.67060.09252.55520.13760.16540.1135-0.2761-0.1533-0.1162-0.1819-0.26020.01570.23260.01790.08820.2263-0.04870.19672.383-22.235-45.094
131.78370.910.52541.14140.62271.75130.05880.0256-0.1143-0.1220.1172-0.1226-0.13680.3041-0.1760.05640.0082-0.04880.3561-0.1170.3138-10.319-10.798-88.724
143.5847-1.05460.90931.5478-0.96211.14990.0849-0.1190.57030.1611-0.17060.0498-0.1038-0.01530.08570.06170.0480.02570.2737-0.17340.3261-27.5864.269-75.568
151.22350.67140.18952.7527-2.24962.4079-0.0992-0.07920.05430.44770.41050.2671-0.5259-0.5398-0.31130.13140.19050.03830.4869-0.01510.229717.854-29.496-82.958
163.15080.43091.70280.93440.26142.5420.0942-0.1735-0.05270.306-0.1413-0.16450.2582-0.32680.04710.1907-0.0129-0.13660.2189-0.03630.174143.536-34.365-90.291
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A332 - 701
2X-RAY DIFFRACTION2B0 - 110
3X-RAY DIFFRACTION3C333 - 701
4X-RAY DIFFRACTION4D0 - 111
5X-RAY DIFFRACTION5E333 - 701
6X-RAY DIFFRACTION6F0 - 112
7X-RAY DIFFRACTION7G333 - 530
8X-RAY DIFFRACTION8H-2 - 111
9X-RAY DIFFRACTION9I333 - 530
10X-RAY DIFFRACTION10J-2 - 111
11X-RAY DIFFRACTION11K333 - 530
12X-RAY DIFFRACTION12L0 - 111
13X-RAY DIFFRACTION13M333 - 530
14X-RAY DIFFRACTION14N-1 - 111
15X-RAY DIFFRACTION15O333 - 529
16X-RAY DIFFRACTION16P1 - 111

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