6ZLR

Soaking competent crystal form of the SARS-CoV-2 Receptor Binding Domain (RBD):CR3022 complex.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6W41 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.72930.1 M SODIUM MALONATE, 0.1 M TRIS PH 7.7, 22% W/V POLYETHYLENE GLYCOL 1,000
Crystal Properties
Matthews coefficientSolvent content
5.1376.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 207.13α = 90
b = 207.13β = 90
c = 199.866γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2020-05-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.9999DiamondI24

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
13.0968.02891.10.9334.64.772060
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.093.1690.60.4151.54.6

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-VALUE6W413.168.02871615366990.5250.2190.21760.247255.64
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]
0.0630.063-0.125
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.099
r_dihedral_angle_3_deg16.873
r_dihedral_angle_4_deg16.11
r_lrange_it13.544
r_lrange_other13.544
r_scangle_it8.243
r_scangle_other8.243
r_mcangle_it8.047
r_mcangle_other8.047
r_dihedral_angle_1_deg7.622
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.099
r_dihedral_angle_3_deg16.873
r_dihedral_angle_4_deg16.11
r_lrange_it13.544
r_lrange_other13.544
r_scangle_it8.243
r_scangle_other8.243
r_mcangle_it8.047
r_mcangle_other8.047
r_dihedral_angle_1_deg7.622
r_scbond_it5.153
r_scbond_other5.149
r_mcbond_it4.992
r_mcbond_other4.992
r_angle_refined_deg1.548
r_angle_other_deg1.227
r_symmetry_nbd_refined0.21
r_nbd_other0.192
r_symmetry_nbd_other0.189
r_symmetry_xyhbond_nbd_refined0.187
r_xyhbond_nbd_refined0.185
r_nbd_refined0.183
r_nbtor_refined0.169
r_symmetry_nbtor_other0.078
r_chiral_restr0.057
r_ncsr_local_group_90.039
r_ncsr_local_group_50.031
r_ncsr_local_group_80.03
r_ncsr_local_group_40.029
r_ncsr_local_group_60.027
r_ncsr_local_group_10.025
r_ncsr_local_group_70.024
r_ncsr_local_group_20.023
r_ncsr_local_group_30.023
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 Atoms14694
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms42

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing