6XA4

Crystal structure of the SARS-CoV-2 (COVID-19) main protease in complex with UAW241


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
1.9837.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 113.538α = 90
b = 54.204β = 100.71
c = 45.414γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2020-05-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.978APS19-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
11.655098.20.0650.0750.0368.24.132214
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)
11.651.6894.10.6330.7480.3890.6753.3

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 6YB71.6538.5430615159997.910.20020.19820.2393RANDOM30.825
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]
1.9-1.05-0.24-1.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.896
r_dihedral_angle_4_deg22.873
r_dihedral_angle_3_deg14.557
r_dihedral_angle_1_deg7.653
r_angle_refined_deg1.631
r_angle_other_deg1.393
r_chiral_restr0.079
r_bond_refined_d0.01
r_gen_planes_refined0.009
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.896
r_dihedral_angle_4_deg22.873
r_dihedral_angle_3_deg14.557
r_dihedral_angle_1_deg7.653
r_angle_refined_deg1.631
r_angle_other_deg1.393
r_chiral_restr0.079
r_bond_refined_d0.01
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 Atoms2343
Nucleic Acid Atoms
Solvent Atoms159
Heterogen Atoms33

Software

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