7LBN

X-ray crystal structure of the SARS-CoV-2 main protease with Calpain I Inhibitor


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52930.2M sodium citrate, 15% PEG3350, 20mM HEPES pH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.7855.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 97.481α = 90
b = 80.729β = 114.36
c = 51.579γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2020-11-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCHESS BEAMLINE A11CHESSA1

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
11.7650970.0380.90538.43.23505523.88
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.761.7972.40.2950.9053.92.4

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 REPLACEMENTTHROUGHOUT6WTK1.7643.2533044200097.690.161250.159790.18546RANDOM33.246
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]
0.020.20.15-0.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.999
r_dihedral_angle_4_deg14.56
r_dihedral_angle_3_deg12.148
r_long_range_B_refined7.759
r_long_range_B_other7.675
r_dihedral_angle_1_deg6.895
r_scangle_other3.683
r_scbond_it2.608
r_scbond_other2.6
r_mcangle_it2.371
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.999
r_dihedral_angle_4_deg14.56
r_dihedral_angle_3_deg12.148
r_long_range_B_refined7.759
r_long_range_B_other7.675
r_dihedral_angle_1_deg6.895
r_scangle_other3.683
r_scbond_it2.608
r_scbond_other2.6
r_mcangle_it2.371
r_mcangle_other2.371
r_angle_refined_deg1.576
r_mcbond_it1.567
r_mcbond_other1.566
r_angle_other_deg1.472
r_chiral_restr0.084
r_bond_refined_d0.01
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2297
Nucleic Acid Atoms
Solvent Atoms303
Heterogen Atoms32

Software

Software
Software NamePurpose
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
REFMACrefinement