6XBI

Crystal structure of the SARS-CoV-2 (COVID-19) main protease in complex with inhibitor UAW248


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6YB7PDB entry 6YB7

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.629820% PEG3000, 0.1 M sodium citrate, pH 5.6
Crystal Properties
Matthews coefficientSolvent content
1.9837.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.898α = 60.63
b = 54.903β = 79.77
c = 62.261γ = 88.83
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2020-05-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.987APS19-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
11.75085.20.0830.98523.992.858337
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)
11.71.730.510.6272.36

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 REPLACEMENTTHROUGHOUTPDB entry 6YB71.747.7549857262390.010.17530.17320.2166RANDOM26.328
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]
-0.810.220.351.880.28-0.35
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.847
r_dihedral_angle_4_deg16.398
r_dihedral_angle_3_deg14.053
r_dihedral_angle_1_deg7.492
r_angle_refined_deg1.696
r_angle_other_deg1.436
r_chiral_restr0.094
r_bond_refined_d0.013
r_gen_planes_refined0.009
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.847
r_dihedral_angle_4_deg16.398
r_dihedral_angle_3_deg14.053
r_dihedral_angle_1_deg7.492
r_angle_refined_deg1.696
r_angle_other_deg1.436
r_chiral_restr0.094
r_bond_refined_d0.013
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4696
Nucleic Acid Atoms
Solvent Atoms384
Heterogen Atoms101

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing