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PanDDA analysis group deposition -- Crystal Structure of Zika virus NS3 Helicase in complex with Z1324080698
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6MH3 6mh3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298
Crystal Properties Matthews coefficient Solvent content 2.15 42.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.348 α = 90 b = 69.134 β = 92.55 c = 57.087 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2018-09-29 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91587 Diamond I04-1
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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.73 57.03 99.3 0.127 0.152 0.082 0.994 7.3 3.3 43318
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) Redundancy Number Unique Reflections (All) 1 1.73 1.82 99.3 1.008 1.22 0.679 0.419 3.1 6311
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (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 Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 6mh3 1.73 57.03 41324 1982 99.25 0.1872 0.185 0.1966 0.2345 0.2471 RANDOM 20.296
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] -1.01 -0.72 0.47 0.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.795 r_dihedral_angle_4_deg 14.409 r_dihedral_angle_3_deg 13.053 r_dihedral_angle_1_deg 6.411 r_mcangle_it 2.637 r_mcbond_it 1.683 r_mcbond_other 1.683 r_angle_refined_deg 1.585 r_angle_other_deg 1.39 r_chiral_restr 0.081
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.795 r_dihedral_angle_4_deg 14.409 r_dihedral_angle_3_deg 13.053 r_dihedral_angle_1_deg 6.411 r_mcangle_it 2.637 r_mcbond_it 1.683 r_mcbond_other 1.683 r_angle_refined_deg 1.585 r_angle_other_deg 1.39 r_chiral_restr 0.081 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3425 Nucleic Acid Atoms Solvent Atoms 420 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing