9HAJ | pdb_00009haj

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 DROP298Morpheus B3
Crystal Properties
Matthews coefficientSolvent content
2.6152.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.046α = 90
b = 99.654β = 90
c = 104.145γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16M2022-12-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA1.00SLSX06DA

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
11.27657.0399.80.1360.0480.9978.26183140
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)
11.2761.29998.12.771.010.3710.7

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-VALUE1.27657.03182872910199.5930.1650.1640.17470.19180.197616.904
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]
-0.358-0.1870.546
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg14.846
r_dihedral_angle_3_deg10.779
r_lrange_it10.46
r_lrange_other8.98
r_dihedral_angle_2_deg6.968
r_dihedral_angle_1_deg6.866
r_scangle_it5.683
r_scangle_other5.682
r_mcangle_other4.43
r_mcangle_it4.429
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg14.846
r_dihedral_angle_3_deg10.779
r_lrange_it10.46
r_lrange_other8.98
r_dihedral_angle_2_deg6.968
r_dihedral_angle_1_deg6.866
r_scangle_it5.683
r_scangle_other5.682
r_mcangle_other4.43
r_mcangle_it4.429
r_scbond_it3.765
r_scbond_other3.764
r_mcbond_it2.867
r_mcbond_other2.856
r_rigid_bond_restr2.251
r_angle_refined_deg1.489
r_angle_other_deg0.532
r_nbd_refined0.209
r_nbd_other0.2
r_symmetry_nbd_other0.195
r_nbtor_refined0.181
r_symmetry_nbd_refined0.18
r_symmetry_xyhbond_nbd_refined0.169
r_ncsr_local_group_10.122
r_xyhbond_nbd_refined0.113
r_xyhbond_nbd_other0.099
r_symmetry_nbtor_other0.081
r_chiral_restr0.076
r_gen_planes_refined0.007
r_bond_refined_d0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4696
Nucleic Acid Atoms
Solvent Atoms644
Heterogen Atoms67

Software

Software
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing