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PanDDA analysis -- Crystal Structure of Zika virus NS3 Helicase in complex with Z56772132
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6MH3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 11.5% PEG 1000 11.5% PEG 3350 11.5% MPD 0.09 M NPS 0.1 M MES-imidazole pH 6.7
Crystal Properties Matthews coefficient Solvent content 2.16 43.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.97 α = 90 b = 68.68 β = 92.42 c = 57.15 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 M 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) 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 1.41 53.98 98.87 0.999 13.29 1.8 79378
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.41 1.46 0.591
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.41 53.98 75442 3934 98.87 0.17022 0.16838 0.20624 0.2213 RANDOM 20.172
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 -0.48 0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.149 r_dihedral_angle_4_deg 15.914 r_dihedral_angle_3_deg 12.613 r_dihedral_angle_1_deg 6.418 r_long_range_B_refined 6.2 r_long_range_B_other 6.199 r_scangle_other 3.628 r_scbond_it 2.416 r_scbond_other 2.416 r_mcangle_it 2.209
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.149 r_dihedral_angle_4_deg 15.914 r_dihedral_angle_3_deg 12.613 r_dihedral_angle_1_deg 6.418 r_long_range_B_refined 6.2 r_long_range_B_other 6.199 r_scangle_other 3.628 r_scbond_it 2.416 r_scbond_other 2.416 r_mcangle_it 2.209 r_mcangle_other 2.209 r_angle_refined_deg 2.12 r_angle_other_deg 1.551 r_mcbond_other 1.494 r_mcbond_it 1.493 r_chiral_restr 0.296 r_bond_refined_d 0.015 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 Atoms Number Protein Atoms 3425 Nucleic Acid Atoms Solvent Atoms 475 Heterogen Atoms 73
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing