7HZP | pdb_00007hzp

Group deposition of Coxsackievirus A16 (G-10) 2A protease in complex with inhibitors from the ASAP AViDD centre -- Crystal structure of Coxsackievirus A16 (G-10) 2A protease in complex with ASAP-0031281-001 (A71EV2A-x2846)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 8POA 

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
2.6753.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.68α = 90
b = 58.239β = 90.81
c = 32.887γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 9M2024-09-25SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.92206DiamondI04-1

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
11.5744.3499.90.7750.8430.3270.9361.86.723372
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)
11.571.661009.9912.084.7830.3886.3

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 REPLACEMENTTHROUGHOUT1.644.371658491479.380.264430.261340.27580.321160.3243RANDOM12.506
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]
0.060.050.4-0.46
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.183
r_dihedral_angle_4_deg19.779
r_dihedral_angle_3_deg15.132
r_long_range_B_refined7.221
r_long_range_B_other7.219
r_dihedral_angle_1_deg6.884
r_mcangle_it1.433
r_mcangle_other1.433
r_angle_refined_deg1.421
r_angle_other_deg1.188
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.183
r_dihedral_angle_4_deg19.779
r_dihedral_angle_3_deg15.132
r_long_range_B_refined7.221
r_long_range_B_other7.219
r_dihedral_angle_1_deg6.884
r_mcangle_it1.433
r_mcangle_other1.433
r_angle_refined_deg1.421
r_angle_other_deg1.188
r_scangle_other1.086
r_mcbond_other0.705
r_mcbond_it0.685
r_scbond_it0.673
r_scbond_other0.655
r_chiral_restr0.05
r_bond_refined_d0.005
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms1083
Nucleic Acid Atoms
Solvent Atoms232
Heterogen Atoms34

Software

Software
Software NamePurpose
REFMACrefinement
REFMAC5refinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction