7BAK

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


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 16% polyethylene glycol mw.3350
Crystal Properties
Matthews coefficientSolvent content
1.9837.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 113.2α = 90
b = 53.78β = 101.45
c = 44.92γ = 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
12.0548.4499.50.0480.0580.0310.99812.43.416661
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)
12.052.111000.6880.8140.430.6993.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT6y2e2.0548.391583182999.420.2010.20.2193RANDOM46.883
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]
1.09-1.130.86-1.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.055
r_dihedral_angle_4_deg16.774
r_dihedral_angle_3_deg15.451
r_dihedral_angle_1_deg7.924
r_angle_refined_deg1.505
r_angle_other_deg1.364
r_chiral_restr0.066
r_bond_refined_d0.007
r_gen_planes_refined0.007
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.055
r_dihedral_angle_4_deg16.774
r_dihedral_angle_3_deg15.451
r_dihedral_angle_1_deg7.924
r_angle_refined_deg1.505
r_angle_other_deg1.364
r_chiral_restr0.066
r_bond_refined_d0.007
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2324
Nucleic Acid Atoms
Solvent Atoms88
Heterogen Atoms1

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing