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PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of NUDT5 in complex with Z768399682
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6GRU 6GRU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 33 % PEG4k, 0.2 MgCl2 and 0.1 M Tris
Crystal Properties Matthews coefficient Solvent content 2.42 49.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.594 α = 79.45 b = 59.884 β = 81.18 c = 79.674 γ = 75.37
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 2018-07-07 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 1.85 77.82 96.5 0.048 0.068 0.048 0.997 7.1 1.7 71290
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 1.85 1.9 95.4 0.573 0.81 0.573 0.674 1.8 5223
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 6GRU 1.85 77.83 67706 3566 96.31 0.2442 0.2419 0.2555 0.2884 0.2957 RANDOM 37.669
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] 3.08 1.34 -0.2 -0.65 0.98 -1.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.432 r_dihedral_angle_4_deg 17.872 r_dihedral_angle_3_deg 16.779 r_dihedral_angle_1_deg 7.236 r_mcangle_it 4.296 r_mcbond_other 2.851 r_mcbond_it 2.84 r_angle_refined_deg 1.787 r_angle_other_deg 1.021 r_chiral_restr 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.432 r_dihedral_angle_4_deg 17.872 r_dihedral_angle_3_deg 16.779 r_dihedral_angle_1_deg 7.236 r_mcangle_it 4.296 r_mcbond_other 2.851 r_mcbond_it 2.84 r_angle_refined_deg 1.787 r_angle_other_deg 1.021 r_chiral_restr 0.1 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5721 Nucleic Acid Atoms Solvent Atoms 247 Heterogen Atoms 81
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing