7C7P

Crystal structure of the SARS-CoV-2 main protease in complex with Telaprevir


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3SNB 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29113% PEG4000, 0.1 M MES pH6.0
Crystal Properties
Matthews coefficientSolvent content
2.5150.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.907α = 90
b = 98.731β = 90
c = 103.487γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2020-05-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL19U10.978531SSRFBL19U1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.7419.8199.90.0980.02122.825.871966
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.741.771001.9250.390.7942.224.5

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 REPLACEMENTTHROUGHOUT3SNB1.7419.8168358351899.820.17620.17420.2159RANDOM30.62
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]
-1.62.29-0.69
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.032
r_dihedral_angle_4_deg19.893
r_dihedral_angle_3_deg16.458
r_dihedral_angle_1_deg7.058
r_angle_refined_deg1.748
r_angle_other_deg1.52
r_chiral_restr0.091
r_bond_refined_d0.011
r_gen_planes_refined0.01
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.032
r_dihedral_angle_4_deg19.893
r_dihedral_angle_3_deg16.458
r_dihedral_angle_1_deg7.058
r_angle_refined_deg1.748
r_angle_other_deg1.52
r_chiral_restr0.091
r_bond_refined_d0.011
r_gen_planes_refined0.01
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4650
Nucleic Acid Atoms
Solvent Atoms526
Heterogen Atoms76

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing