6ZH9

Ternary complex CR3022 H11-H4 and RBD (SARS-CoV-2)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293mixing 0.2 uL of the 18 mg/mL complex with 0.1 uL of the crystallization buffer containing 0.2 M Sodium acetate trihydrate, 0.1 M MES pH 6.0, 20 % w/v PEG 8000.
Crystal Properties
Matthews coefficientSolvent content
4.2270.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 156.411α = 90
b = 156.411β = 90
c = 116.205γ = 90
Symmetry
Space GroupP 42 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2020-06-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.98DiamondI03

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
13.3180.2531000.09110.01825.622105
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.313.43.90.770.30.5

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-VALUE6ZBY3.3180.24322065108899.9640.2630.26090.3052134
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]
-1.696-1.6963.392
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.97
r_dihedral_angle_1_deg21.543
r_dihedral_angle_other_3_deg20.671
r_lrange_it19.804
r_lrange_other19.804
r_dihedral_angle_4_deg17.991
r_dihedral_angle_3_deg17.099
r_mcangle_it12.289
r_mcangle_other12.288
r_scangle_it11.809
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.97
r_dihedral_angle_1_deg21.543
r_dihedral_angle_other_3_deg20.671
r_lrange_it19.804
r_lrange_other19.804
r_dihedral_angle_4_deg17.991
r_dihedral_angle_3_deg17.099
r_mcangle_it12.289
r_mcangle_other12.288
r_scangle_it11.809
r_scangle_other11.808
r_mcbond_it7.791
r_mcbond_other7.787
r_scbond_it7.25
r_scbond_other7.249
r_angle_refined_deg1.626
r_angle_other_deg1.228
r_symmetry_xyhbond_nbd_refined0.266
r_nbd_other0.254
r_symmetry_nbd_other0.188
r_nbd_refined0.185
r_symmetry_nbd_refined0.179
r_nbtor_refined0.174
r_xyhbond_nbd_refined0.143
r_symmetry_nbtor_other0.077
r_xyhbond_nbd_other0.074
r_chiral_restr0.059
r_bond_refined_d0.008
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5856
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
pointlessdata scaling
PHASERphasing