7H3Z | pdb_00007h3z

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 Z1216861874 (A71EV2A-x0525)


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
2.3848.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86.088α = 90
b = 56.539β = 95.26
c = 32.421γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 16M2023-10-11SINGLE 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
11.1947.1999.40.1350.1460.0550.9989.26.849334
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)
11.191.2198.92.7322.9651.1370.3696.7

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 REPLACEMENTTHROUGHOUT1.1947.246757240699.020.173920.173110.180.188890.19RANDOM16.172
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]
-0.06-0.420.41-0.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.521
r_dihedral_angle_4_deg24.16
r_dihedral_angle_3_deg12.561
r_dihedral_angle_1_deg6.733
r_long_range_B_other5.229
r_long_range_B_refined5.221
r_scangle_other3.187
r_angle_other_deg2.44
r_scbond_it2.271
r_scbond_other2.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.521
r_dihedral_angle_4_deg24.16
r_dihedral_angle_3_deg12.561
r_dihedral_angle_1_deg6.733
r_long_range_B_other5.229
r_long_range_B_refined5.221
r_scangle_other3.187
r_angle_other_deg2.44
r_scbond_it2.271
r_scbond_other2.27
r_mcangle_other2.134
r_mcangle_it2.123
r_angle_refined_deg2.065
r_mcbond_other1.404
r_mcbond_it1.399
r_chiral_restr0.112
r_bond_other_d0.036
r_gen_planes_other0.021
r_bond_refined_d0.014
r_gen_planes_refined0.013
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 Atoms1083
Nucleic Acid Atoms
Solvent Atoms237
Heterogen Atoms33

Software

Software
Software NamePurpose
REFMACrefinement
REFMAC5refinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction