7VIC

The crystal structure of SARS-CoV-2 3C-like protease in complex with a traditional Chinese Medicine Inhibitors


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6LU7 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP289100 mM MES, pH6, 12% PEG 6000, 0.5% DMSO
Crystal Properties
Matthews coefficientSolvent content
2.8556.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.178α = 90
b = 81.411β = 96.14
c = 91.218γ = 90
Symmetry
Space GroupI 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDOXFORD ONYX CCD2021-04-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SEALED TUBEOXFORD DIFFRACTION NOVA1.5406

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
12.124.49999.70.1290.99110.54.422123
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.180.814

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 REPLACEMENTTHROUGHOUT6LU72.124.49922123113399.5630.2170.21590.242231.129
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]
0.0250.001-0.009-0.016
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.754
r_dihedral_angle_3_deg14.662
r_dihedral_angle_4_deg7.348
r_dihedral_angle_1_deg6.781
r_lrange_other4.206
r_lrange_it4.179
r_angle_other_deg2.361
r_mcangle_it2.09
r_mcangle_other2.089
r_scangle_it1.664
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.754
r_dihedral_angle_3_deg14.662
r_dihedral_angle_4_deg7.348
r_dihedral_angle_1_deg6.781
r_lrange_other4.206
r_lrange_it4.179
r_angle_other_deg2.361
r_mcangle_it2.09
r_mcangle_other2.089
r_scangle_it1.664
r_scangle_other1.663
r_angle_refined_deg1.22
r_mcbond_it1.166
r_mcbond_other1.165
r_scbond_it0.975
r_scbond_other0.974
r_symmetry_nbd_other0.221
r_nbd_refined0.211
r_nbtor_refined0.158
r_symmetry_xyhbond_nbd_refined0.143
r_nbd_other0.134
r_xyhbond_nbd_refined0.11
r_symmetry_nbd_refined0.081
r_symmetry_nbtor_other0.065
r_chiral_restr0.048
r_bond_other_d0.036
r_gen_planes_refined0.003
r_gen_planes_other0.003
r_bond_refined_d0.002
r_symmetry_xyhbond_nbd_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2295
Nucleic Acid Atoms
Solvent Atoms103
Heterogen Atoms26

Software

Software
Software NamePurpose
REFMACrefinement
CrysalisProdata reduction
CrysalisProdata scaling
PHASERphasing