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PanDDA analysis group deposition -- Crystal Structure of NUDT5 in complex with 1R-0641
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6GRU PDB entry 6GRU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293.15 33% PEG4000, 0.2 magnesium chloride, 0.1 M Tris
Crystal Properties Matthews coefficient Solvent content 2.41 48.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.26 α = 79.47 b = 59.871 β = 81.46 c = 79.887 γ = 75.59
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 2019-04-22 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 1.67 41.48 94.2 0.033 0.047 0.033 0.999 9.5 1.7 95026
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 1.67 1.76 93.9 0.885 1.251 0.885 0.432 1.5 13864
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT PDB entry 6GRU 1.67 41.52 89541 4724 93.41 0.231 0.2294 0.2618 0.2786 RANDOM 38.281
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] 2.83 1.15 0.16 -0.65 0.58 -1.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.375 r_dihedral_angle_3_deg 15.977 r_dihedral_angle_4_deg 13.147 r_dihedral_angle_1_deg 7.547 r_mcangle_it 4.103 r_mcbond_other 2.654 r_mcbond_it 2.64 r_angle_refined_deg 1.518 r_angle_other_deg 1.297 r_chiral_restr 0.064
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.375 r_dihedral_angle_3_deg 15.977 r_dihedral_angle_4_deg 13.147 r_dihedral_angle_1_deg 7.547 r_mcangle_it 4.103 r_mcbond_other 2.654 r_mcbond_it 2.64 r_angle_refined_deg 1.518 r_angle_other_deg 1.297 r_chiral_restr 0.064 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5784 Nucleic Acid Atoms Solvent Atoms 256 Heterogen Atoms 93
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing