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PanDDA analysis group deposition -- Crystal Structure of human NUDT22 in complex with N13910a
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5LF9 5LF9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 0.1M HEPES pH 7.5, 0.3M sodium/potassium phosphate, 15% PEG Smear High, 20% ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.01 38.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.41 α = 90 b = 52.26 β = 90 c = 101.6 γ = 90
Symmetry Space Group P 21 21 21
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 2016-07-03 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 1.53 24.64 99.9 0.086 0.093 0.037 0.999 10.4 6.4 40491
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 1.53 1.57 99.8 1.704 1.849 0.714 0.5 6.6 2935
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 5LF9 1.53 24.65 38259 2171 99.81 0.1903 0.1884 0.2032 0.223 0.2376 RANDOM 23.82
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] 1.57 -1.93 0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.097 r_dihedral_angle_4_deg 13.887 r_dihedral_angle_3_deg 12.934 r_dihedral_angle_1_deg 6.727 r_mcangle_it 2.636 r_mcbond_it 1.864 r_mcbond_other 1.841 r_angle_refined_deg 1.577 r_angle_other_deg 1.395 r_chiral_restr 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.097 r_dihedral_angle_4_deg 13.887 r_dihedral_angle_3_deg 12.934 r_dihedral_angle_1_deg 6.727 r_mcangle_it 2.636 r_mcbond_it 1.864 r_mcbond_other 1.841 r_angle_refined_deg 1.577 r_angle_other_deg 1.395 r_chiral_restr 0.08 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2198 Nucleic Acid Atoms Solvent Atoms 163 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing