9RJR | pdb_00009rjr

SARS-CoV-2 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
2.6353.21

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.12α = 90
b = 100.11β = 90
c = 104.31γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2022-06-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA1.0SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.70572.22893.80.1330.038113.613.260607
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.7051.86651.11.9870.570.4581.8

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 REPLACEMENTTHROUGHOUT1.70572.22860607311477.240.1990.19730.19740.22930.229330.608
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]
0.014-0.0580.044
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.381
r_dihedral_angle_6_deg16.228
r_dihedral_angle_2_deg9.808
r_lrange_it8.46
r_lrange_other8.457
r_dihedral_angle_1_deg7.431
r_scangle_it6.617
r_scangle_other6.576
r_scbond_it4.38
r_scbond_other4.343
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.381
r_dihedral_angle_6_deg16.228
r_dihedral_angle_2_deg9.808
r_lrange_it8.46
r_lrange_other8.457
r_dihedral_angle_1_deg7.431
r_scangle_it6.617
r_scangle_other6.576
r_scbond_it4.38
r_scbond_other4.343
r_mcangle_it3.976
r_mcangle_other3.976
r_mcbond_it2.857
r_mcbond_other2.854
r_angle_refined_deg1.529
r_angle_other_deg0.511
r_symmetry_nbd_refined0.303
r_symmetry_xyhbond_nbd_refined0.234
r_nbd_refined0.224
r_nbd_other0.213
r_symmetry_nbd_other0.194
r_nbtor_refined0.181
r_metal_ion_refined0.164
r_xyhbond_nbd_refined0.142
r_ncsr_local_group_10.112
r_symmetry_nbtor_other0.082
r_chiral_restr0.075
r_symmetry_xyhbond_nbd_other0.013
r_gen_planes_refined0.008
r_bond_refined_d0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4676
Nucleic Acid Atoms
Solvent Atoms291
Heterogen Atoms57

Software

Software
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing