7Z0P

SARS-COV2 Main Protease in complex with inhibitor MG-131


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP92930.1 M MMT, pH 9.0 plus 25% w/v polyethylenglycol 1500
Crystal Properties
Matthews coefficientSolvent content
1.9436.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 113.716α = 90
b = 51.667β = 103.335
c = 45.451γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2021-12-16MSINGLE 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
12.5246.81990.040.99916.23.549867
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)
12.522.620.996

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-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE6y2e2.5246.81875242098.7810.2080.20350.289844.003
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]
1.881-1.2830.932-1.982
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.076
r_dihedral_angle_4_deg22.426
r_dihedral_angle_3_deg19.084
r_dihedral_angle_1_deg9.324
r_lrange_it7.922
r_lrange_other7.921
r_dihedral_angle_other_3_deg7.442
r_scangle_it5.183
r_scangle_other5.182
r_mcangle_it4.981
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.076
r_dihedral_angle_4_deg22.426
r_dihedral_angle_3_deg19.084
r_dihedral_angle_1_deg9.324
r_lrange_it7.922
r_lrange_other7.921
r_dihedral_angle_other_3_deg7.442
r_scangle_it5.183
r_scangle_other5.182
r_mcangle_it4.981
r_mcangle_other4.979
r_scbond_it3.171
r_scbond_other3.17
r_mcbond_other3.151
r_mcbond_it3.15
r_angle_refined_deg1.592
r_angle_other_deg1.185
r_symmetry_xyhbond_nbd_refined0.256
r_chiral_restr0.252
r_nbd_refined0.225
r_nbd_other0.221
r_symmetry_nbd_other0.193
r_xyhbond_nbd_refined0.179
r_nbtor_refined0.172
r_symmetry_nbd_refined0.15
r_symmetry_nbtor_other0.078
r_symmetry_xyhbond_nbd_other0.033
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2347
Nucleic Acid Atoms
Solvent Atoms37
Heterogen Atoms41

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing