☰ Navigation Tabs
PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of NUDT5 in complex with Z198194396
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 2.43 49.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.535 α = 79.16 b = 59.991 β = 81.16 c = 80.05 γ = 75.31
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 2018-07-28 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 1.57 34.91 94.7 0.03 0.043 0.03 0.998 10 1.7 115029
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 1.57 1.66 94 0.945 1.336 0.944 0.515 1.5 16672
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 1.57 78.13 109238 5790 94.74 0.2336 0.2318 0.246 0.2671 0.276 RANDOM 34.677
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 0.89 -0.27 -0.61 0.99 -1.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.897 r_dihedral_angle_3_deg 15.299 r_dihedral_angle_4_deg 12.905 r_dihedral_angle_1_deg 7.172 r_mcangle_it 4.249 r_mcbond_other 3.066 r_mcbond_it 3.044 r_angle_refined_deg 1.983 r_angle_other_deg 1.041 r_chiral_restr 0.118
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.897 r_dihedral_angle_3_deg 15.299 r_dihedral_angle_4_deg 12.905 r_dihedral_angle_1_deg 7.172 r_mcangle_it 4.249 r_mcbond_other 3.066 r_mcbond_it 3.044 r_angle_refined_deg 1.983 r_angle_other_deg 1.041 r_chiral_restr 0.118 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5733 Nucleic Acid Atoms Solvent Atoms 250 Heterogen Atoms 73
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing