☰ Navigation Tabs
PanDDA analysis group deposition -- Crystal Structure of NUDT5 in complex with GB-0804
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 2.42 49.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.33 α = 79.34 b = 59.82 β = 81.47 c = 80.18 γ = 75.65
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 2019-04-20 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 78.34 96.6 0.068 0.096 0.068 0.986 8.3 1.8 87469
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 95.2 0.726 1.027 0.726 0.639 1.6 6388
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 1.73 78.34 83055 4414 96.53 0.223 0.2214 0.2329 0.2534 0.2578 RANDOM 36.351
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] 2.87 0.78 -0.26 -0.73 1.65 -1.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.067 r_dihedral_angle_3_deg 16.716 r_dihedral_angle_4_deg 13.638 r_dihedral_angle_1_deg 7.296 r_mcangle_it 3.73 r_mcbond_other 2.452 r_mcbond_it 2.427 r_angle_refined_deg 1.502 r_angle_other_deg 1.295 r_chiral_restr 0.063
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.067 r_dihedral_angle_3_deg 16.716 r_dihedral_angle_4_deg 13.638 r_dihedral_angle_1_deg 7.296 r_mcangle_it 3.73 r_mcbond_other 2.452 r_mcbond_it 2.427 r_angle_refined_deg 1.502 r_angle_other_deg 1.295 r_chiral_restr 0.063 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 5847 Nucleic Acid Atoms Solvent Atoms 288 Heterogen Atoms 77
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing