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PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of NUDT7 in complex with NUOOA000301a
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5T3P 5T3P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 0.1M bis-tris pH 5.5 -- 0.1M ammonium acetate -- 5%(w/v) PEG10K
Crystal Properties Matthews coefficient Solvent content 4.15 70.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.659 α = 90 b = 124.659 β = 90 c = 41.113 γ = 120
Symmetry Space Group P 3 2 1
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 2017-10-25 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 1.67 28.96 99.9 0.071 0.075 0.024 0.997 18.6 9.9 42833
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 1.67 1.71 98.7 0.703 0.75 0.26 0.885 8.2 3114
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 5T3P 1.67 107.96 40741 2091 99.87 0.1953 0.1944 0.2048 0.2125 0.2217 RANDOM 32.241
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.546 r_dihedral_angle_4_deg 18.107 r_dihedral_angle_3_deg 13.654 r_dihedral_angle_1_deg 6.172 r_mcangle_it 3.523 r_mcbond_it 2.379 r_mcbond_other 2.377 r_angle_refined_deg 1.744 r_angle_other_deg 0.977 r_chiral_restr 0.114
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.546 r_dihedral_angle_4_deg 18.107 r_dihedral_angle_3_deg 13.654 r_dihedral_angle_1_deg 6.172 r_mcangle_it 3.523 r_mcbond_it 2.379 r_mcbond_other 2.377 r_angle_refined_deg 1.744 r_angle_other_deg 0.977 r_chiral_restr 0.114 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1467 Nucleic Acid Atoms Solvent Atoms 162 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing