7GOY | pdb_00007goy

PanDDA analysis group deposition -- Crystal Structure of Enterovirus D68 3C Protease in complex with Z375990520


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.1429825% PEG 3350, 0.1M Tris, 0.2M Ammonium acetate
Crystal Properties
Matthews coefficientSolvent content
2.4549.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.771α = 90
b = 62.505β = 90
c = 147.456γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2023-01-26SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.92124DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.6373.7398.60.1430.1480.040.9989.513.549964
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.631.7197.32.5412.6410.7150.46913.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.6373.7347381248298.30.184670.183510.210.207020.24RANDOM26.58
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]
-0.250.010.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.606
r_dihedral_angle_4_deg17.252
r_dihedral_angle_3_deg14.648
r_dihedral_angle_1_deg7.494
r_long_range_B_refined6.852
r_long_range_B_other6.747
r_scangle_other4.678
r_mcangle_other3.157
r_mcangle_it3.154
r_scbond_it2.816
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.606
r_dihedral_angle_4_deg17.252
r_dihedral_angle_3_deg14.648
r_dihedral_angle_1_deg7.494
r_long_range_B_refined6.852
r_long_range_B_other6.747
r_scangle_other4.678
r_mcangle_other3.157
r_mcangle_it3.154
r_scbond_it2.816
r_scbond_other2.815
r_mcbond_it2.037
r_mcbond_other2.03
r_angle_refined_deg1.533
r_angle_other_deg1.356
r_chiral_restr0.077
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_gen_planes_other0.002
r_bond_other_d0.001
r_nbd_refined
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_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2808
Nucleic Acid Atoms
Solvent Atoms303
Heterogen Atoms36

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction