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PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of NUDT7 in complex with RK4-332
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 4.16 70.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.7 α = 90 b = 124.7 β = 90 c = 41.19 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 2017-09-22 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.97628 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 1.57 54 99.8 0.052 0.054 0.016 0.999 20.9 11.2 51396
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 1.57 1.61 99.7 2.003 2.101 0.631 0.654 11 3749
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 1.57 108.23 48696 2694 99.8 0.2007 0.2 0.2092 0.213 0.2253 RANDOM 35.569
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] 0.58 0.29 0.58 -1.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.107 r_dihedral_angle_4_deg 14.829 r_dihedral_angle_3_deg 12.907 r_dihedral_angle_1_deg 5.947 r_mcangle_it 3.272 r_mcbond_it 2.147 r_mcbond_other 2.146 r_angle_refined_deg 1.508 r_angle_other_deg 0.917 r_chiral_restr 0.092
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.107 r_dihedral_angle_4_deg 14.829 r_dihedral_angle_3_deg 12.907 r_dihedral_angle_1_deg 5.947 r_mcangle_it 3.272 r_mcbond_it 2.147 r_mcbond_other 2.146 r_angle_refined_deg 1.508 r_angle_other_deg 0.917 r_chiral_restr 0.092 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 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 156 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing