7BAL

Crystal structure of SARS-CoV-2 main protease treated with ebselen derivative of MR6-31-2


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP292200mM ammonium chloride, 5%glycerol and 20% polyethylene glycol mw. 3350
Crystal Properties
Matthews coefficientSolvent content
1.9837.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 114.004α = 90
b = 53.622β = 100.892
c = 44.545γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 16Mmirrors2020-08-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9795DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
11.8533.86799.90.0750.1020.0690.9978.63.322635
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.851.8999.91.0791.4560.9710.4461.63.2

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-VALUE6y2e1.8533.86722624115999.810.2250.22390.24936.114
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]
2.4010.48-0.621-1.829
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.358
r_dihedral_angle_4_deg15.983
r_dihedral_angle_3_deg15.115
r_dihedral_angle_1_deg7.769
r_lrange_it7.584
r_scangle_it5.721
r_mcangle_it4.314
r_scbond_it4.084
r_mcbond_it3.288
r_angle_refined_deg1.572
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.358
r_dihedral_angle_4_deg15.983
r_dihedral_angle_3_deg15.115
r_dihedral_angle_1_deg7.769
r_lrange_it7.584
r_scangle_it5.721
r_mcangle_it4.314
r_scbond_it4.084
r_mcbond_it3.288
r_angle_refined_deg1.572
r_symmetry_nbd_refined0.426
r_nbtor_refined0.321
r_symmetry_xyhbond_nbd_refined0.249
r_nbd_refined0.219
r_xyhbond_nbd_refined0.17
r_chiral_restr0.103
r_gen_planes_refined0.008
r_bond_refined_d0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2307
Nucleic Acid Atoms
Solvent Atoms139
Heterogen Atoms1

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing