7NBR

Crystal structure of SARS-CoV-2 main protease (Mpro) in complex with the HCV NS3/4A inhibitor boceprevir


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5293.150.2 M Sodium acetate trihydrate, 0.1 M Sodium cacodylate pH 6.5, 30% PEG 8000
Crystal Properties
Matthews coefficientSolvent content
2.0239.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 113.767α = 90
b = 53.37β = 101.833
c = 45.949γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2020-06-09MSINGLE 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)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
12.448.1399.90.0930.1010.0390.99915.66.710684
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.531000.4960.6636.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE6Y2E2.434.441068451299.850.1840.18010.269452.68
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]
1.0820.5931.961-3.026
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.343
r_dihedral_angle_3_deg17.398
r_dihedral_angle_4_deg15.229
r_lrange_it8.787
r_lrange_other8.787
r_dihedral_angle_1_deg8.379
r_scangle_it6.353
r_scangle_other6.351
r_mcangle_it6.169
r_mcangle_other6.138
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.343
r_dihedral_angle_3_deg17.398
r_dihedral_angle_4_deg15.229
r_lrange_it8.787
r_lrange_other8.787
r_dihedral_angle_1_deg8.379
r_scangle_it6.353
r_scangle_other6.351
r_mcangle_it6.169
r_mcangle_other6.138
r_mcbond_it4.334
r_mcbond_other4.309
r_scbond_it4.218
r_scbond_other4.217
r_angle_refined_deg1.927
r_angle_other_deg1.496
r_symmetry_xyhbond_nbd_refined0.226
r_nbd_refined0.219
r_nbd_other0.199
r_symmetry_nbd_other0.187
r_xyhbond_nbd_refined0.177
r_nbtor_refined0.172
r_symmetry_nbd_refined0.172
r_chiral_restr0.171
r_symmetry_nbtor_other0.082
r_xyhbond_nbd_other0.038
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_dihedral_angle_other_3_deg0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2319
Nucleic Acid Atoms
Solvent Atoms48
Heterogen Atoms38

Software

Software
Software NamePurpose
REFMACrefinement
MOLREPphasing
SCALAdata scaling