9HJH | pdb_00009hjh

Structure of compound 1 bound to SARS-CoV-2 main protease


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherinternal structure

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29325% PEG 3350, 0.1M HEPES pH 7.0
Crystal Properties
Matthews coefficientSolvent content
2.6453.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.799α = 90
b = 101.274β = 90
c = 104.099γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE CdTe 16M2024-04-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.89ESRFID23-1

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
11.19756.999.90.10.050.99611.39.9223287
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)
11.1971.2180.7280.3670.8742.3

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-VALUE1.256.8772120471124299.9940.150.14950.16440.15930.170214.58
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]
1.614-1.232-0.382
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg14.766
r_lrange_it10.653
r_dihedral_angle_3_deg10.524
r_lrange_other9.164
r_dihedral_angle_1_deg6.935
r_dihedral_angle_2_deg5.045
r_scangle_it4.698
r_scangle_other4.698
r_mcangle_other4.102
r_mcangle_it4.1
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4673
Nucleic Acid Atoms
Solvent Atoms688
Heterogen Atoms82

Software

Software
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing