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PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of NUDT7 in complex with FMOPL000476a
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 4.28 71.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 125.83 α = 90 b = 125.83 β = 90 c = 41.53 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 1.55 31.46 99.9 0.095 0.101 0.032 0.998 13.6 10 54854
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 1.55 1.59 99.9 2.251 2.368 0.733 0.587 10.4 4038
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 1.55 108.97 52048 2803 99.91 0.1657 0.1642 0.1638 0.1951 0.1952 RANDOM 32.119
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] 0.12 0.06 0.12 -0.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.837 r_sphericity_free 26.545 r_dihedral_angle_4_deg 16.654 r_dihedral_angle_3_deg 13.763 r_sphericity_bonded 11.167 r_dihedral_angle_1_deg 5.748 r_mcangle_it 3.488 r_rigid_bond_restr 3.329 r_mcbond_it 2.819 r_mcbond_other 2.784
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.837 r_sphericity_free 26.545 r_dihedral_angle_4_deg 16.654 r_dihedral_angle_3_deg 13.763 r_sphericity_bonded 11.167 r_dihedral_angle_1_deg 5.748 r_mcangle_it 3.488 r_rigid_bond_restr 3.329 r_mcbond_it 2.819 r_mcbond_other 2.784 r_angle_refined_deg 1.753 r_angle_other_deg 0.986 r_chiral_restr 0.117 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 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 175 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing