7H4J

Group deposition for crystallographic fragment screening of Coxsackievirus A16 (G-10) 2A protease -- Crystal structure of Coxsackievirus A16 (G-10) 2A protease in complex with Z53825020 (A71EV2A-x0875)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.05293.150.1 M MES, pH 6.05, 16 % PEG 20,000
Crystal Properties
Matthews coefficientSolvent content
2.1743.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.729α = 90
b = 60.911β = 93.07
c = 32.396γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 16M2023-12-03SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.94054DiamondI03

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
11.7946.6599.50.3210.3470.130.9885.2713305
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)
11.791.8398.12.7142.9491.1380.2656.6

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 REPLACEMENTTHROUGHOUT1.7946.671264460898.960.221130.220060.24569RANDOM29.489
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]
0.78-0.260.52-1.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.759
r_dihedral_angle_4_deg20.728
r_dihedral_angle_3_deg17.278
r_dihedral_angle_1_deg7.338
r_long_range_B_refined6.63
r_long_range_B_other6.555
r_mcangle_it3.428
r_mcangle_other3.428
r_scangle_other2.863
r_mcbond_other1.857
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.759
r_dihedral_angle_4_deg20.728
r_dihedral_angle_3_deg17.278
r_dihedral_angle_1_deg7.338
r_long_range_B_refined6.63
r_long_range_B_other6.555
r_mcangle_it3.428
r_mcangle_other3.428
r_scangle_other2.863
r_mcbond_other1.857
r_mcbond_it1.854
r_scbond_it1.788
r_scbond_other1.768
r_angle_refined_deg1.467
r_angle_other_deg1.246
r_chiral_restr0.072
r_bond_refined_d0.01
r_gen_planes_refined0.007
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 Atoms1065
Nucleic Acid Atoms
Solvent Atoms55
Heterogen Atoms33

Software

Software
Software NamePurpose
REFMACrefinement
REFMAC5refinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction