☰ Navigation Tabs
PanDDA analysis group deposition -- Crystal Structure of NUDT5 in complex with FS-3764
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 = 48.992 α = 79.35 b = 59.76 β = 81.73 c = 80.343 γ = 75.91
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 1.55 41.24 94.4 0.023 0.032 0.023 0.999 12.2 1.6 118554
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 1.55 1.59 79 0.454 0.642 0.454 0.783 1.4 7390
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 PDB entry 6GRU 1.55 35.06 112510 5989 94.28 0.1991 0.1978 0.2098 0.2239 0.2335 RANDOM 29.903
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] 2.31 0.85 0.53 -0.57 0.55 -0.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.87 r_dihedral_angle_3_deg 14.75 r_dihedral_angle_4_deg 13.519 r_dihedral_angle_1_deg 7.163 r_mcangle_it 3.321 r_mcbond_other 2.349 r_mcbond_it 2.347 r_angle_refined_deg 1.606 r_angle_other_deg 1.401 r_chiral_restr 0.073
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.87 r_dihedral_angle_3_deg 14.75 r_dihedral_angle_4_deg 13.519 r_dihedral_angle_1_deg 7.163 r_mcangle_it 3.321 r_mcbond_other 2.349 r_mcbond_it 2.347 r_angle_refined_deg 1.606 r_angle_other_deg 1.401 r_chiral_restr 0.073 r_bond_refined_d 0.01 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 5876 Nucleic Acid Atoms Solvent Atoms 406 Heterogen Atoms 84
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing