9F3A

Crystal structure of SARS-CoV-2 Mpro in complex with RK-325


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6Y2E 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.2 M Sodium bromide, 0.1 M Bis-Tris propane pH8.5, 20% w/v PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.0640.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.257α = 90
b = 62.879β = 94.083
c = 97.495γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2023-04-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, DESY BEAMLINE P111.0332PETRA III, DESYP11

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.1548.6299.180.9976.3729646
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.152.2270.559

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)Mean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2.1548.6229645143899.1970.2130.21010.21440.27840.282734.372
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]
-1.9210.8871.3240.466
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg17.135
r_dihedral_angle_6_deg14.698
r_dihedral_angle_2_deg9.477
r_dihedral_angle_1_deg8.209
r_lrange_other7.234
r_lrange_it7.23
r_dihedral_angle_other_3_deg5.51
r_scangle_it5.28
r_scangle_other5.279
r_mcangle_it4.308
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4691
Nucleic Acid Atoms
Solvent Atoms138
Heterogen Atoms76

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing