9F2X

Crystal structure of SARS-CoV-2 Mpro in complex with RHTCR03


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72930.1M HEPES pH 7.0, 2M Sodium chloride, 20% w/v PEG 6000, 10% v/v Ethylene glycol
Crystal Properties
Matthews coefficientSolvent content
2.2344.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.78α = 90
b = 63.55β = 90.88
c = 103.31γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2022-03-03MSINGLE 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)R Merge I (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
11.945.7898.780.0790.9989.83.946402
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)
11.91.9680.758

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-VALUE1.945.7846402210198.7570.1780.17540.18490.22550.235628.308
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]
-0.4750.0660.775-0.302
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg15.757
r_dihedral_angle_3_deg15.716
r_dihedral_angle_2_deg10.139
r_dihedral_angle_1_deg7.352
r_lrange_it6.82
r_lrange_other6.758
r_scangle_it5.19
r_scangle_other5.19
r_mcangle_it3.409
r_mcangle_other3.409
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4707
Nucleic Acid Atoms
Solvent Atoms343
Heterogen Atoms72

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing