6XBG

Crystal structure of the SARS-CoV-2 (COVID-19) main protease in complex with inhibitor UAW246


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7BRRPDB entry 7BRR

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.629820% PEG3000, 0.1 M sodium citrate, pH 5.6
Crystal Properties
Matthews coefficientSolvent content
2.2344.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.367α = 90
b = 98.854β = 108.23
c = 59.215γ = 90
Symmetry
Space GroupP 1 21 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)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
11.455098.70.0860.0990.0499.53.9105029
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)
11.451.4898.81.0631.2320.6150.1423.7

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 7BRR1.4537.1599703529798.440.18260.18140.2057RANDOM22.598
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]
0.44-0.81-0.540.52
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.748
r_dihedral_angle_4_deg14.986
r_dihedral_angle_3_deg13.443
r_dihedral_angle_1_deg7.512
r_angle_refined_deg1.832
r_angle_other_deg1.499
r_chiral_restr0.091
r_bond_refined_d0.014
r_gen_planes_refined0.011
r_gen_planes_other0.004
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.748
r_dihedral_angle_4_deg14.986
r_dihedral_angle_3_deg13.443
r_dihedral_angle_1_deg7.512
r_angle_refined_deg1.832
r_angle_other_deg1.499
r_chiral_restr0.091
r_bond_refined_d0.014
r_gen_planes_refined0.011
r_gen_planes_other0.004
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4658
Nucleic Acid Atoms
Solvent Atoms426
Heterogen Atoms95

Software

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