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PanDDA analysis group deposition -- Crystal Structure of Zika virus NS3 Helicase in complex with Z3241250482
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5RHY 5RHY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 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 2.21 44.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.613 α = 90 b = 69.968 β = 92.53 c = 57.678 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 2022-12-02 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 1.81 44.49 99.9 0.144 0.156 0.059 0.996 7.1 7 38877 32.89
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 1.81 1.85 98.9 2.503 2.699 1.001 0.33 7.2
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 5RHY 1.809 25.86 38736 1770 99.4 0.2024 0.2 0.1929 0.253 0.2435 RANDOM 38.48
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] 8.3573 -6.9213 -0.4105 -7.9468
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.99 t_omega_torsion 3.14 t_angle_deg 0.91 t_bond_d 0.009 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.99 t_omega_torsion 3.14 t_angle_deg 0.91 t_bond_d 0.009 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle 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 364 Heterogen Atoms 33
Software Software Software Name Purpose BUSTER refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing