7C8R

Complex Structure of SARS-CoV-2 3CL Protease with TG-0203770


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2ZU4 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP429310% PEG 4000, 0.1 M sodium acetate trihydrate, pH 4.0.
Crystal Properties
Matthews coefficientSolvent content
2.141.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 104.39α = 90
b = 104.39β = 90
c = 90.233γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDRAYONIX MX300-HS2020-03-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE TPS 05A1.0NSRRCTPS 05A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.32599.80.9222.911.613388
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)
12.32.380.92

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-VALUE2ZU42.324.171334368199.5370.2030.20020.248331.468
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]
0.0560.0280.056-0.183
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.213
r_dihedral_angle_4_deg20.87
r_dihedral_angle_3_deg15.168
r_dihedral_angle_1_deg8.495
r_lrange_it7.261
r_lrange_other7.26
r_scangle_it4.256
r_scangle_other4.255
r_dihedral_angle_other_3_deg4.106
r_mcangle_it3.653
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.213
r_dihedral_angle_4_deg20.87
r_dihedral_angle_3_deg15.168
r_dihedral_angle_1_deg8.495
r_lrange_it7.261
r_lrange_other7.26
r_scangle_it4.256
r_scangle_other4.255
r_dihedral_angle_other_3_deg4.106
r_mcangle_it3.653
r_mcangle_other3.652
r_scbond_it2.77
r_scbond_other2.769
r_mcbond_other2.391
r_mcbond_it2.39
r_angle_refined_deg1.625
r_angle_other_deg1.297
r_symmetry_nbd_refined0.238
r_nbd_other0.226
r_nbd_refined0.199
r_symmetry_nbd_other0.198
r_xyhbond_nbd_refined0.192
r_symmetry_xyhbond_nbd_refined0.173
r_nbtor_refined0.169
r_symmetry_xyhbond_nbd_other0.155
r_symmetry_nbtor_other0.079
r_chiral_restr0.071
r_bond_refined_d0.008
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 Atoms2329
Nucleic Acid Atoms
Solvent Atoms84
Heterogen Atoms45

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing