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PanDDA analysis group deposition -- Crystal Structure of NUDT5 in complex with AE-0227
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 49.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.246 α = 79.42 b = 59.826 β = 81.55 c = 80.052 γ = 75.7
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 2019-05-03 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 1.73 42.63 96.3 0.041 0.058 0.041 0.991 8.9 1.7 87066
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 1.73 1.77 94.5 0.659 0.932 0.659 0.461 1.5 6333
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 1.73 42.67 82657 4372 96.17 0.2301 0.2285 0.261 0.2796 RANDOM 33.59
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] 2.93 1.15 -0.02 -1.07 0.73 -0.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.597 r_dihedral_angle_3_deg 16.121 r_dihedral_angle_4_deg 13.305 r_dihedral_angle_1_deg 7.53 r_mcangle_it 3.934 r_mcbond_it 2.784 r_mcbond_other 2.784 r_angle_refined_deg 1.615 r_angle_other_deg 1.316 r_chiral_restr 0.072
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.597 r_dihedral_angle_3_deg 16.121 r_dihedral_angle_4_deg 13.305 r_dihedral_angle_1_deg 7.53 r_mcangle_it 3.934 r_mcbond_it 2.784 r_mcbond_other 2.784 r_angle_refined_deg 1.615 r_angle_other_deg 1.316 r_chiral_restr 0.072 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5814 Nucleic Acid Atoms Solvent Atoms 258 Heterogen Atoms 105
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing