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- PDB-7k8n: Crystal structure of an anti-SARS-CoV-2 human neutralizing antibo... -

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Database: PDB / ID: 7k8n
TitleCrystal structure of an anti-SARS-CoV-2 human neutralizing antibody Fab fragment, C102
  • C102 Fab Heavy Chain
  • C102 Fab Light Chain
KeywordsIMMUNE SYSTEM / Human Neutralizing Antibody / SARS-CoV-2 / Receptor Binding Domain / COVID-19
Biological speciesHomo sapiens (human)
AuthorsJette, C.A. / Barnes, C.O. / Bjorkman, P.J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01-AI138938-S1 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P50 AI150464-13 United States
Validation Report
SummaryFull reportAbout validation report
DepositionSep 27, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2020Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Jan 13, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

Structure visualization

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Deposited unit
A: C102 Fab Heavy Chain
B: C102 Fab Light Chain
hetero molecules

Theoretical massNumber of molelcules
Total (without water)47,55812

TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4880 Å2
ΔGint-54 kcal/mol
Surface area19590 Å2
Unit cell
Length a, b, c (Å)88.813, 88.813, 218.858
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6


Antibody , 2 types, 2 molecules AB

#1: Antibody C102 Fab Heavy Chain

Mass: 23296.098 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Antibody C102 Fab Light Chain

Mass: 23314.793 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)

Non-polymers , 4 types, 111 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate

Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical

Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol

Mass: 106.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H10O3
#6: Water ChemComp-HOH / water / Water

Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O


Has ligand of interestN

Experimental details


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

Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.2 M ammonium sulfate, 20% w/v PEG3350

Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.65→38.04 Å / Num. obs: 116041 / % possible obs: 99.9 % / Redundancy: 19.2 % / Biso Wilson estimate: 28.45 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.023 / Net I/σ(I): 15.3
Reflection shellResolution: 1.65→1.71 Å / Rmerge(I) obs: 1.48 / Num. unique obs: 6095 / CC1/2: 0.807 / Rpim(I) all: 0.334


Blu-Icedata collection
DIALSdata reduction
xia2data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 7BZ5
Resolution: 1.65→38.04 Å / SU ML: 0.1871 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.9768
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2072 3745 3.23 %
Rwork0.1965 112296 -
Obs0.1968 116041 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.51 Å2
Refinement stepCycle: LAST / Resolution: 1.65→38.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3244 0 58 101 3403
Refine LS restraints
Refinement-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01513380
X-RAY DIFFRACTIONf_angle_d1.44274589
X-RAY DIFFRACTIONf_chiral_restr0.0739508
X-RAY DIFFRACTIONf_plane_restr0.0097585
X-RAY DIFFRACTIONf_dihedral_angle_d19.87391206
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefinement-ID% reflection obs (%)
1.65-1.670.35691320.32424146X-RAY DIFFRACTION99.74
1.67-1.690.28821380.28154144X-RAY DIFFRACTION100
1.69-1.720.23151410.25764167X-RAY DIFFRACTION100
1.72-1.740.2721390.25234146X-RAY DIFFRACTION100
1.74-1.770.26011420.24094156X-RAY DIFFRACTION100
1.77-1.790.24891390.22554179X-RAY DIFFRACTION100
1.79-1.820.27491340.22494136X-RAY DIFFRACTION100
1.82-1.860.2321430.2154200X-RAY DIFFRACTION100
1.86-1.890.21481360.21814152X-RAY DIFFRACTION100
1.89-1.930.24541360.21284182X-RAY DIFFRACTION100
1.93-1.960.18931400.20664115X-RAY DIFFRACTION100
1.97-2.010.24691370.20044160X-RAY DIFFRACTION99.98
2.01-2.050.19451410.20864167X-RAY DIFFRACTION100
2.05-2.110.26161380.20524174X-RAY DIFFRACTION100
2.11-2.160.18911400.20784151X-RAY DIFFRACTION100
2.16-2.230.25491340.20924159X-RAY DIFFRACTION100
2.23-2.30.25861410.21874140X-RAY DIFFRACTION100
2.3-2.380.2721410.21324164X-RAY DIFFRACTION99.98
2.38-2.480.20871440.2174177X-RAY DIFFRACTION99.98
2.48-2.590.21491350.21294149X-RAY DIFFRACTION100
2.59-2.720.2441400.21624151X-RAY DIFFRACTION100
2.72-2.90.21521410.21664161X-RAY DIFFRACTION100
2.9-3.120.2541350.21354156X-RAY DIFFRACTION100
3.12-3.430.19181350.20234183X-RAY DIFFRACTION100
3.43-3.930.16721430.18264148X-RAY DIFFRACTION100
3.93-4.940.1781380.14374175X-RAY DIFFRACTION100
4.95-38.040.16981420.17764158X-RAY DIFFRACTION99.86
Refinement TLS params.

Method: refined / Refinement-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)
Refinement TLS group
IDRefinement-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 112)
2X-RAY DIFFRACTION2chain 'A' and (resid 113 through 214)
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 108 )
4X-RAY DIFFRACTION4chain 'B' and (resid 109 through 213)

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