6YZ7

H11-D4, SARS-CoV-2 RBD, CR3022 ternary complex


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6YLA 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION298The best crystals were grown in condition containing 0.1 M sodium citrate tribasic dihydrate, pH 5.0, 10% (w/v) Polyethylene glycol 6000.
Crystal Properties
Matthews coefficientSolvent content
3.9268.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 154.598α = 90
b = 154.598β = 90
c = 229.312γ = 90
Symmetry
Space GroupP 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2020-04-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.978DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
13.29128.187980.0940.9944.97840954
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.293.354.0940.369

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE6YLA3.3128.18740954193996.2920.2390.23770.2688144.159
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]
-1.97-1.973.94
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.684
r_dihedral_angle_3_deg17.533
r_dihedral_angle_4_deg14.96
r_dihedral_angle_1_deg7.668
r_lrange_it4.952
r_lrange_other4.951
r_mcangle_it2.879
r_mcangle_other2.879
r_scangle_it2.857
r_scangle_other2.857
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.684
r_dihedral_angle_3_deg17.533
r_dihedral_angle_4_deg14.96
r_dihedral_angle_1_deg7.668
r_lrange_it4.952
r_lrange_other4.951
r_mcangle_it2.879
r_mcangle_other2.879
r_scangle_it2.857
r_scangle_other2.857
r_mcbond_other1.679
r_mcbond_it1.678
r_scbond_it1.6
r_scbond_other1.6
r_angle_refined_deg1.39
r_angle_other_deg1.126
r_symmetry_xyhbond_nbd_other0.32
r_nbd_other0.237
r_symmetry_nbd_refined0.236
r_nbd_refined0.206
r_symmetry_nbd_other0.179
r_nbtor_refined0.169
r_xyhbond_nbd_refined0.164
r_symmetry_nbtor_other0.073
r_ncsr_local_group_20.063
r_chiral_restr0.049
r_ncsr_local_group_10.046
r_ncsr_local_group_30.042
r_ncsr_local_group_40.014
r_bond_refined_d0.004
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11686
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling