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PanDDA analysis group deposition -- Crystal Structure of Zika virus NS3 Helicase in complex with Z2856434938
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 42.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.28 α = 90 b = 69.44 β = 92.33 c = 56.99 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 1.61 44.03 99.8 0.053 0.063 0.034 0.999 11.9 3.2 53682
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 1.61 1.65 99.6 0.861 1.076 0.637 0.514 2.6 3980
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 1.61 44.07 51111 2549 99.69 0.172 0.1701 0.1833 0.2115 0.2236 RANDOM 26.952
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] 0.71 -1.6 -1.2 0.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.802 r_dihedral_angle_4_deg 14.963 r_dihedral_angle_3_deg 13.508 r_dihedral_angle_1_deg 6.408 r_mcangle_it 3.162 r_mcbond_it 2.178 r_mcbond_other 2.178 r_angle_refined_deg 1.668 r_angle_other_deg 1.435 r_chiral_restr 0.087
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.802 r_dihedral_angle_4_deg 14.963 r_dihedral_angle_3_deg 13.508 r_dihedral_angle_1_deg 6.408 r_mcangle_it 3.162 r_mcbond_it 2.178 r_mcbond_other 2.178 r_angle_refined_deg 1.668 r_angle_other_deg 1.435 r_chiral_restr 0.087 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 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 421 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing