☰ Navigation Tabs
PanDDA analysis group deposition -- Crystal Structure of NUDT5 in complex with FS-2639
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 49.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.27 α = 79.33 b = 59.808 β = 81.48 c = 80.068 γ = 75.66
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 1.79 47.47 96.5 0.047 0.066 0.047 0.997 8.8 1.8 78713
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 1.79 1.84 95.6 0.966 1.366 0.966 0.322 1.7 5770
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 1.79 47.5 74669 3972 96.21 0.2156 0.214 0.2472 0.258 RANDOM 32.479
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] 2.47 0.65 0.18 -0.4 0.93 -1.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.655 r_dihedral_angle_3_deg 15.162 r_dihedral_angle_4_deg 12.645 r_dihedral_angle_1_deg 7.531 r_mcangle_it 3.563 r_mcbond_it 2.344 r_mcbond_other 2.344 r_angle_refined_deg 1.477 r_angle_other_deg 1.303 r_chiral_restr 0.062
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.655 r_dihedral_angle_3_deg 15.162 r_dihedral_angle_4_deg 12.645 r_dihedral_angle_1_deg 7.531 r_mcangle_it 3.563 r_mcbond_it 2.344 r_mcbond_other 2.344 r_angle_refined_deg 1.477 r_angle_other_deg 1.303 r_chiral_restr 0.062 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 5818 Nucleic Acid Atoms Solvent Atoms 275 Heterogen Atoms 89
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing