5ZUV

Crystal Structure of the Human Coronavirus 229E HR1 motif in complex with pan-CoVs inhibitor EK1


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION7.52930.05M MgCl2, 0.1M HEPES, pH 7.5, 30% PEG550MME
Crystal Properties
Matthew coefficientSolvent content
2.4349.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.515α = 90
b = 45.548β = 96.33
c = 94.737γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2016-10-20MSINGLE 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)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
12.2144.499.40.0870.040.97918.94.72044128
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.212.2999.50.2170.0974.5

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 REPLACEMENTTHROUGHOUT2bez2.2131.3919426102098.750.20420.20190.24809RANDOM42.831
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]
5.521.44-1.89-3.85
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.087
r_dihedral_angle_3_deg14.299
r_dihedral_angle_4_deg10.673
r_long_range_B_refined6.904
r_dihedral_angle_1_deg4.392
r_scbond_it3.319
r_mcangle_it3.075
r_mcbond_it2.039
r_angle_refined_deg1.259
r_chiral_restr0.081
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.087
r_dihedral_angle_3_deg14.299
r_dihedral_angle_4_deg10.673
r_long_range_B_refined6.904
r_dihedral_angle_1_deg4.392
r_scbond_it3.319
r_mcangle_it3.075
r_mcbond_it2.039
r_angle_refined_deg1.259
r_chiral_restr0.081
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_bond_other_d
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_sphericity_bonded
r_mcbond_other
r_angle_other_deg
r_mcangle_other
r_gen_planes_other
r_scbond_other
r_scangle_it
r_scangle_other
r_nbd_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_symmetry_vdw_refined
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2950
Nucleic Acid Atoms
Solvent Atoms110
Heterogen Atoms2

Software

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