7C8U

The crystal structure of COVID-19 main protease in complex with GC376


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1Q2W 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72930.2M Lithium chloride, 0.1M Hepes pH 7, 20% w/v PEG 6000
Crystal Properties
Matthews coefficientSolvent content
2.0339.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 114.303α = 90
b = 53.874β = 101.576
c = 45.233γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2020-03-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08ID-10.97949CLSI08ID-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
12.3548.5799.20.0650.0650.0360.9989.7311269
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)
12.352.430.3470.4180.230.889

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 REPLACEMENTNONE1q2w2.3544.3521122656398.7420.2150.21150.272840.478
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]
-0.013-0.0130.017
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.104
r_dihedral_angle_4_deg15.332
r_dihedral_angle_3_deg13.32
r_dihedral_angle_1_deg6.949
r_dihedral_angle_other_3_deg5.499
r_lrange_it4.984
r_lrange_other4.984
r_mcangle_it2.895
r_mcangle_other2.892
r_scangle_other2.844
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.104
r_dihedral_angle_4_deg15.332
r_dihedral_angle_3_deg13.32
r_dihedral_angle_1_deg6.949
r_dihedral_angle_other_3_deg5.499
r_lrange_it4.984
r_lrange_other4.984
r_mcangle_it2.895
r_mcangle_other2.892
r_scangle_other2.844
r_scangle_it2.624
r_angle_other_deg2.391
r_mcbond_it1.715
r_mcbond_other1.709
r_scbond_it1.568
r_scbond_other1.567
r_angle_refined_deg1.247
r_symmetry_nbd_refined0.217
r_symmetry_nbd_other0.209
r_nbd_refined0.191
r_nbd_other0.191
r_nbtor_refined0.157
r_xyhbond_nbd_refined0.148
r_symmetry_xyhbond_nbd_refined0.148
r_symmetry_xyhbond_nbd_other0.071
r_symmetry_nbtor_other0.062
r_chiral_restr0.046
r_bond_other_d0.036
r_gen_planes_refined0.004
r_gen_planes_other0.004
r_bond_refined_d0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2323
Nucleic Acid Atoms
Solvent Atoms57
Heterogen Atoms29

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing