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PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of NUDT7 in complex with FMOPL000710a
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 4.34 71.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 126.501 α = 90 b = 126.501 β = 90 c = 41.716 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 0.92819 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 1.95 29.39 99.8 0.05 0.052 0.016 0.999 28 10.1 28189
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 1.95 2 98.4 0.673 0.71 0.223 0.917 10.1 2053
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 1.95 109.55 26400 1357 98.68 0.1933 0.1917 0.2012 0.2236 0.2315 RANDOM 39.686
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] 0.24 0.12 0.24 -0.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.316 r_dihedral_angle_4_deg 18.738 r_dihedral_angle_3_deg 14.732 r_dihedral_angle_1_deg 6.39 r_mcangle_it 4.367 r_mcbond_it 3.258 r_mcbond_other 3.216 r_angle_refined_deg 1.809 r_angle_other_deg 1.007 r_chiral_restr 0.117
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.316 r_dihedral_angle_4_deg 18.738 r_dihedral_angle_3_deg 14.732 r_dihedral_angle_1_deg 6.39 r_mcangle_it 4.367 r_mcbond_it 3.258 r_mcbond_other 3.216 r_angle_refined_deg 1.809 r_angle_other_deg 1.007 r_chiral_restr 0.117 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1467 Nucleic Acid Atoms Solvent Atoms 170 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing