8C9O

Crystal structure of SARS-CoV-2 Mpro-S144A mutant in complex with 13b-K


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5298Ethylene glycols, HEPES, PEG 500 MME, PEG 20000
Crystal Properties
Matthews coefficientSolvent content
2.5852.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.766α = 90
b = 99.689β = 90
c = 103.307γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293PIXELDECTRIS PILATUS 6M-F2022-05-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, DESY BEAMLINE P111.003PETRA 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
11.6949.3199.880.99913.7113.47887231.02
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.7699.73.380.426

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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-VALUE6y2e1.6949.3178872381999.8530.20.19840.210.23440.2438.737
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]
-1.8742.545-0.671
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.55
r_dihedral_angle_4_deg16.321
r_dihedral_angle_3_deg15.29
r_lrange_it7.883
r_lrange_other7.874
r_dihedral_angle_1_deg7.788
r_scangle_it5.996
r_scangle_other5.995
r_mcangle_it4.825
r_mcangle_other4.825
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4705
Nucleic Acid Atoms
Solvent Atoms261
Heterogen Atoms86

Software

Software
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
Aimlessdata scaling
PHENIXphasing