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PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of NUDT7 in complex with UNUYB062989
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 4.12 70.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.333 α = 90 b = 124.333 β = 90 c = 41.009 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 2017-05-11 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 1.59 29.86 99.9 0.05 0.052 0.016 0.999 24.9 11.2 48790
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 1.59 1.63 98.7 0.824 0.865 0.258 0.864 11 3573
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 5T3P 1.59 107.91 46200 2589 99.87 0.1956 0.1948 0.2103 0.2266 RANDOM 31.948
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] 0.28 0.14 0.28 -0.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.286 r_dihedral_angle_4_deg 14.681 r_dihedral_angle_3_deg 13.269 r_dihedral_angle_1_deg 5.858 r_mcangle_it 3.235 r_mcbond_it 2.09 r_mcbond_other 2.069 r_angle_refined_deg 1.558 r_angle_other_deg 0.932 r_chiral_restr 0.097
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.286 r_dihedral_angle_4_deg 14.681 r_dihedral_angle_3_deg 13.269 r_dihedral_angle_1_deg 5.858 r_mcangle_it 3.235 r_mcbond_it 2.09 r_mcbond_other 2.069 r_angle_refined_deg 1.558 r_angle_other_deg 0.932 r_chiral_restr 0.097 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 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 160 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing