7HOV | pdb_00007hov

PanDDA analysis group deposition -- Crystal Structure of ZIKV NS2B-NS3 protease in complex with ASAP-0014707-001


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.829830% w/v PEG 2000, 0.2M Ammonium sulfate, 0.1M acetate (pH 4.8)
Crystal Properties
Matthews coefficientSolvent content
2.1141.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.508α = 90
b = 42.508β = 90
c = 216.455γ = 90
Symmetry
Space GroupP 43 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 9M2023-09-19SINGLE 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
11.69216.461000.2330.2370.0470.9996.425.523551
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.691.7299.916.3653.1760.50826.3

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 REPLACEMENTTHROUGHOUT1.6954.111890899784.890.231250.228890.24040.275650.2762RANDOM53.248
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]
2.522.52-5.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.737
r_dihedral_angle_4_deg18.912
r_dihedral_angle_3_deg17.481
r_long_range_B_refined8.584
r_long_range_B_other8.485
r_dihedral_angle_1_deg8.302
r_scangle_other3.073
r_mcangle_other2.911
r_mcangle_it2.91
r_scbond_other1.728
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.737
r_dihedral_angle_4_deg18.912
r_dihedral_angle_3_deg17.481
r_long_range_B_refined8.584
r_long_range_B_other8.485
r_dihedral_angle_1_deg8.302
r_scangle_other3.073
r_mcangle_other2.911
r_mcangle_it2.91
r_scbond_other1.728
r_scbond_it1.726
r_angle_refined_deg1.629
r_mcbond_other1.617
r_mcbond_it1.603
r_angle_other_deg1.238
r_chiral_restr0.066
r_bond_refined_d0.011
r_gen_planes_refined0.008
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 Atoms1476
Nucleic Acid Atoms
Solvent Atoms96
Heterogen Atoms47

Software

Software
Software NamePurpose
REFMACrefinement
BUSTERrefinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction
XDSdata reduction
XDSdata reduction
XDSdata reduction
XDSdata reduction