7GPY

PanDDA analysis group deposition -- Crystal Structure of Enterovirus D68 3C Protease in complex with NCL-00024667


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
2.4649.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.69α = 90
b = 62.786β = 90
c = 147.71γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2023-01-27SINGLE 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
11.573.861000.1110.1160.0320.99711.31364727
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)
11.51.5899.92.1962.3070.6970.50310.6

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.573.8661615298899.820.190770.189780.21018RANDOM24.28
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]
0.290.07-0.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.818
r_dihedral_angle_4_deg15.813
r_dihedral_angle_3_deg14.153
r_dihedral_angle_1_deg7.077
r_long_range_B_refined6.959
r_long_range_B_other6.87
r_scangle_other5.256
r_mcangle_it3.518
r_mcangle_other3.517
r_scbond_it3.317
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.818
r_dihedral_angle_4_deg15.813
r_dihedral_angle_3_deg14.153
r_dihedral_angle_1_deg7.077
r_long_range_B_refined6.959
r_long_range_B_other6.87
r_scangle_other5.256
r_mcangle_it3.518
r_mcangle_other3.517
r_scbond_it3.317
r_scbond_other3.316
r_mcbond_other2.336
r_mcbond_it2.326
r_angle_refined_deg1.74
r_angle_other_deg1.487
r_chiral_restr0.089
r_bond_refined_d0.011
r_gen_planes_refined0.009
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms311
Heterogen Atoms15

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction