7N3D

Crystal Structure of Human Fab S24-1564 in the complex with the N-terminal Domain of Nucleocapsid protein from SARS CoV-2


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5KKUPDBIDs 5KKU, 5O4G, 6IEB
experimental modelPDB 5O4GPDBIDs 5KKU, 5O4G, 6IEB
experimental modelPDB 6IEBPDBIDs 5KKU, 5O4G, 6IEB

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52980.2 M Magnesium chloride hexahydrate, 0.1 M HEPES pH 7.5, 25% w/v Polyethylene glycol 3,350
Crystal Properties
Matthews coefficientSolvent content
2.2946.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.927α = 90
b = 67.318β = 106.643
c = 86.087γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 X 6M2021-02-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97890APS19-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.525095.90.1140.986224.48161921.23
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.531.5666.20.8340.4120.961.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUEPDBIDs 5KKU, 5O4G, 6IEB1.5339.511.3881560393095.150.15880.15720.190228.84
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d13.467
f_angle_d1.015
f_chiral_restr0.0634
f_bond_d0.0094
f_plane_restr0.0078
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4164
Nucleic Acid Atoms
Solvent Atoms394
Heterogen Atoms34

Software

Software
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MOLREPphasing