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PanDDA analysis group deposition -- Crystal Structure of Zika virus NS3 Helicase in complex with Z126932614
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 42.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.72 α = 90 b = 68.63 β = 92.18 c = 57.05 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 2018-09-26 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 1.5 53.68 99.4 0.059 0.071 0.039 0.998 11 3 65839
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 1.5 1.54 97.5 0.829 1.074 0.675 0.421 2.2 4744
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 1.5 53.74 62624 3194 99.29 0.1725 0.1708 0.1745 0.2085 0.2141 RANDOM 20.878
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] -0.16 0.33 -0.68 0.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.168 r_dihedral_angle_4_deg 13.456 r_dihedral_angle_3_deg 13.027 r_dihedral_angle_1_deg 6.382 r_mcangle_it 2.853 r_mcbond_it 1.87 r_mcbond_other 1.87 r_angle_refined_deg 1.747 r_angle_other_deg 1.499 r_chiral_restr 0.091
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.168 r_dihedral_angle_4_deg 13.456 r_dihedral_angle_3_deg 13.027 r_dihedral_angle_1_deg 6.382 r_mcangle_it 2.853 r_mcbond_it 1.87 r_mcbond_other 1.87 r_angle_refined_deg 1.747 r_angle_other_deg 1.499 r_chiral_restr 0.091 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3425 Nucleic Acid Atoms Solvent Atoms 420 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing