5ZVM

Crystal Structure of the Human Coronavirus SARS HR1 motif in complex with pan-CoVs inhibitor EK1


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION5.52930.2M Li2SO4, 0.1M BIS-Tris, pH 5.5, 25% PEG3350
Crystal Properties
Matthew coefficientSolvent content
2.346.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.958α = 90
b = 100.958β = 90
c = 73.425γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2017-07-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL19U10.9785SSRFBL19U1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim I (All)Rpim I (All)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
13.334.599.90.1720.0611.98.1607097.8
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.33.4210010.3630.741.57.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2bez3.334.5606030799.750.25070.24760.3014RANDOM112
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]
1.361.36-2.73
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.487
r_dihedral_angle_3_deg17.245
r_long_range_B_refined11.898
r_long_range_B_other11.896
r_dihedral_angle_4_deg9.673
r_scangle_other8.236
r_mcangle_it7.207
r_mcangle_other7.205
r_scbond_it4.708
r_scbond_other4.706
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.487
r_dihedral_angle_3_deg17.245
r_long_range_B_refined11.898
r_long_range_B_other11.896
r_dihedral_angle_4_deg9.673
r_scangle_other8.236
r_mcangle_it7.207
r_mcangle_other7.205
r_scbond_it4.708
r_scbond_other4.706
r_dihedral_angle_1_deg4.546
r_mcbond_it4.337
r_mcbond_other4.331
r_angle_other_deg1.381
r_angle_refined_deg1.138
r_chiral_restr0.054
r_bond_refined_d0.009
r_bond_other_d0.005
r_gen_planes_refined0.004
r_gen_planes_other0.003
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_scangle_it
r_metal_ion_refined
r_metal_ion_other
r_sphericity_bonded
r_rigid_bond_restr
r_sphericity_free
r_symmetry_vdw_refined
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2438
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

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