9F2V

Crystal structure of SARS-CoV-2 Mpro in complex with RHTCR02


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52930.1M Bis Tris Propane pH 7.50, 2M Sodium nitrate, 20% w/vPEG 3350 and 10% v/vEthylene glycol
Crystal Properties
Matthews coefficientSolvent content
2.2645.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.852α = 90
b = 63.688β = 91.171
c = 103.506γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2021-11-24MSINGLE 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
12.19145.88498.790.086640.99719.96.9208789
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)
12.1912.270.973

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-VALUE2.19145.88430460149898.7680.1690.16670.17610.20910.220323.194
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]
-1.2030.3940.6340.552
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.412
r_dihedral_angle_6_deg16.329
r_dihedral_angle_2_deg8.006
r_dihedral_angle_1_deg7.474
r_dihedral_angle_other_3_deg6.765
r_lrange_it6.304
r_lrange_other6.303
r_scangle_it4.656
r_scangle_other4.655
r_mcangle_it3.08
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4714
Nucleic Acid Atoms
Solvent Atoms111
Heterogen Atoms74

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing