9GMQ

Crystal structure of the Mpro of SARS COV-2 in complex with the MG-87 inhibitor


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52930.02 M sodium/potassium phosphate, 0.1 M Bis Tris propane pH8.5, 20 % w/v PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.2445.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.941α = 90
b = 63.773β = 91.251
c = 103.513γ = 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)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
12.1945.97298.60.99610.96.930543
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)
12.192.260.852

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-VALUE2.1945.97230543141198.580.1690.16640.17490.21840.223626.817
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]
-0.980.0860.0610.915
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.058
r_dihedral_angle_6_deg15.708
r_dihedral_angle_2_deg9.487
r_dihedral_angle_1_deg7.611
r_lrange_other6.726
r_lrange_it6.725
r_scangle_it5.106
r_scangle_other5.106
r_dihedral_angle_other_3_deg4.427
r_mcangle_other3.481
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4734
Nucleic Acid Atoms
Solvent Atoms181
Heterogen Atoms73

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing