8D4J

Crystal Structure of SARS-CoV-2 Main Protease (Mpro) H172Y Mutant


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7LYH 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP293.1525% PEG 3350, 0.1M Potassium/Sodium Tartrate, 0.005M Magnesium Chloride
Crystal Properties
Matthews coefficientSolvent content
1.9938.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.962α = 90
b = 53.474β = 101.14
c = 114.185γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300-HS2022-04-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-BM1.0APS22-BM

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.785099.50.06324.23.551114
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.781.810.2382.73

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 REPLACEMENTTHROUGHOUT7LYH1.7838.7148410269199.390.1680.16560.2092RANDOM25.226
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]
0.78-0.360.39-0.96
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg13.958
r_dihedral_angle_2_deg10.665
r_dihedral_angle_1_deg6.932
r_angle_refined_deg1.243
r_angle_other_deg0.46
r_chiral_restr0.063
r_gen_planes_refined0.006
r_bond_refined_d0.005
r_bond_other_d0.003
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4685
Nucleic Acid Atoms
Solvent Atoms478
Heterogen Atoms6

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing