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PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of NUDT5 in complex with Z240297434
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 2.39 48.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.728 α = 79.65 b = 59.593 β = 82 c = 80.188 γ = 76.23
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 1.61 78.5 95.3 0.033 0.047 0.033 0.994 9.8 1.7 105862
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 92.8 0.595 0.841 0.595 0.672 1.5 7621
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 1.61 78.48 100519 5310 95.07 0.2113 0.21 0.2215 0.2369 0.2467 RANDOM 30.843
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] 2.53 0.78 0.54 -0.9 0.81 -0.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.814 r_dihedral_angle_3_deg 14.458 r_dihedral_angle_4_deg 12.163 r_dihedral_angle_1_deg 6.439 r_mcangle_it 2.999 r_mcbond_other 1.854 r_mcbond_it 1.8 r_angle_refined_deg 1.569 r_angle_other_deg 0.947 r_chiral_restr 0.092
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.814 r_dihedral_angle_3_deg 14.458 r_dihedral_angle_4_deg 12.163 r_dihedral_angle_1_deg 6.439 r_mcangle_it 2.999 r_mcbond_other 1.854 r_mcbond_it 1.8 r_angle_refined_deg 1.569 r_angle_other_deg 0.947 r_chiral_restr 0.092 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5776 Nucleic Acid Atoms Solvent Atoms 319 Heterogen Atoms 59
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing