9RI0 | pdb_00009ri0

SARS-CoV-2 3CL protease with a bound inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherin-house structure

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29330mM sodium nitrate, 30mM disodium hydrogen phosphate, 30mM ammonium sulfate, 100mM MES-imidazole pH 6.5, 20%(w/v) PEG 550 MME, 10%(w/v) PEG 20K (Morpheus condition C1)
Crystal Properties
Matthews coefficientSolvent content
2.6653.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.86α = 90
b = 101.85β = 90
c = 104.25γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2023-06-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA1.00SLSX10SA

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
11.3972.85396.30.08112.76.6767039
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)
11.391.4970.6960.5991.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)Mean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1.3972.853116189563379.9030.1770.17630.17630.1980.197916.012
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]
-0.0050.017-0.011
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg16.947
r_dihedral_angle_3_deg14.436
r_dihedral_angle_1_deg6.921
r_dihedral_angle_2_deg6.587
r_lrange_it5.917
r_lrange_other5.917
r_scangle_it4.627
r_scangle_other4.622
r_scbond_it3.122
r_scbond_other3.119
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg16.947
r_dihedral_angle_3_deg14.436
r_dihedral_angle_1_deg6.921
r_dihedral_angle_2_deg6.587
r_lrange_it5.917
r_lrange_other5.917
r_scangle_it4.627
r_scangle_other4.622
r_scbond_it3.122
r_scbond_other3.119
r_mcangle_other2.31
r_mcangle_it2.309
r_angle_refined_deg1.715
r_mcbond_it1.626
r_mcbond_other1.626
r_angle_other_deg0.578
r_nbd_refined0.219
r_symmetry_nbd_other0.191
r_nbtor_refined0.184
r_symmetry_nbd_refined0.157
r_nbd_other0.157
r_xyhbond_nbd_refined0.143
r_metal_ion_refined0.132
r_ncsr_local_group_10.129
r_symmetry_xyhbond_nbd_refined0.128
r_chiral_restr0.089
r_symmetry_nbtor_other0.083
r_dihedral_angle_other_3_deg0.022
r_bond_refined_d0.011
r_gen_planes_refined0.011
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4701
Nucleic Acid Atoms
Solvent Atoms604
Heterogen Atoms85

Software

Software
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing