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PanDDA analysis -- Crystal Structure of Zika virus NS3 Helicase in complex with Z203039992
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 0.12 M NPS Mix (0.3 M Sodium phosphate dibasic dihydrate, 0.3 M Ammonium sulphate and 0.3 M Sodium nitrate - Molecular Dimensions), 0.1 M MES/Imidazole pH 6.5 (Molecular Dimensions) and 33% Precipitant Mix 4 (11% MPD, 11% PEG 1,000 e 11% PEG 3,350
Crystal Properties Matthews coefficient Solvent content 2.19 43.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.644 α = 90 b = 69.588 β = 92.19 c = 57.552 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 EIGER X 9M 2022-11-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92124 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 1.925 57.51 100 0.184 0.199 0.076 0.996 7.4 6.8 32130
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 1.93 2.03 100 1.902 2.051 0.764 0.42 7.1
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.925 25.01 32071 1474 99.8 0.1928 0.1906 0.1855 0.239 0.2337 RANDOM 34.27
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] 1.6676 0.7408 0.2318 -1.8994
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.78 t_omega_torsion 3.18 t_angle_deg 0.91 t_bond_d 0.008 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.78 t_omega_torsion 3.18 t_angle_deg 0.91 t_bond_d 0.008 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3433 Nucleic Acid Atoms Solvent Atoms 373 Heterogen Atoms 31
Software Software Software Name Purpose BUSTER refinement Aimless data scaling autoPROC data reduction PHASER phasing