8V7R

PanDDA analysis -- Crystal Structure of Zika virus NS3 Helicase in complex with Z56772132


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6MH3 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION29311.5% PEG 1000 11.5% PEG 3350 11.5% MPD 0.09 M NPS 0.1 M MES-imidazole pH 6.7
Crystal Properties
Matthews coefficientSolvent content
2.1643.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.97α = 90
b = 68.68β = 92.42
c = 57.15γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2018-09-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.91587DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
11.4153.9898.870.99913.291.879378
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.411.460.591

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 REPLACEMENTTHROUGHOUT1.4153.9875442393498.870.170220.168380.20624RANDOM20.172
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]
0.36-0.16-0.480.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.149
r_dihedral_angle_4_deg15.914
r_dihedral_angle_3_deg12.613
r_dihedral_angle_1_deg6.418
r_long_range_B_refined6.2
r_long_range_B_other6.199
r_scangle_other3.628
r_scbond_it2.416
r_scbond_other2.416
r_mcangle_it2.209
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.149
r_dihedral_angle_4_deg15.914
r_dihedral_angle_3_deg12.613
r_dihedral_angle_1_deg6.418
r_long_range_B_refined6.2
r_long_range_B_other6.199
r_scangle_other3.628
r_scbond_it2.416
r_scbond_other2.416
r_mcangle_it2.209
r_mcangle_other2.209
r_angle_refined_deg2.12
r_angle_other_deg1.551
r_mcbond_other1.494
r_mcbond_it1.493
r_chiral_restr0.296
r_bond_refined_d0.015
r_gen_planes_refined0.012
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 Atoms3425
Nucleic Acid Atoms
Solvent Atoms475
Heterogen Atoms73

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing