7Z8O

Crystal structure of SARS-CoV-2 S RBD in complex with a stapled peptide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7CH5 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29222 %v/v PEGSB, 0.1 M Na Phos Cit 5.5 pH
Crystal Properties
Matthews coefficientSolvent content
2.2344.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.163α = 90
b = 55.692β = 90
c = 82.718γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 16M2021-02-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.8DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
10.9646.299.20.0610.0620.014119.618.7123986
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
10.960.9890.41.6271.7760.6850.3746.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT7CH50.9646.2116468613198.160.15280.1520.1691RANDOM15.855
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]
0.030.03-0.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.191
r_rigid_bond_restr14.993
r_dihedral_angle_4_deg13.084
r_dihedral_angle_3_deg11.456
r_dihedral_angle_1_deg7.055
r_angle_refined_deg2.117
r_angle_other_deg1.668
r_chiral_restr0.12
r_bond_refined_d0.019
r_gen_planes_refined0.013
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.191
r_rigid_bond_restr14.993
r_dihedral_angle_4_deg13.084
r_dihedral_angle_3_deg11.456
r_dihedral_angle_1_deg7.055
r_angle_refined_deg2.117
r_angle_other_deg1.668
r_chiral_restr0.12
r_bond_refined_d0.019
r_gen_planes_refined0.013
r_bond_other_d0.004
r_gen_planes_other0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1597
Nucleic Acid Atoms
Solvent Atoms349
Heterogen Atoms70

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction
PHASERphasing