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PanDDA analysis group deposition -- Crystal Structure of human NUDT22 in complex with N14004a
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 2.02 39.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.57 α = 90 b = 52.37 β = 90 c = 101.88 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 2016-07-02 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 1.48 46.58 99.9 0.079 0.086 0.034 0.999 11.5 6.5 45068
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 1.48 1.52 99.8 1.692 1.849 0.738 0.474 6.1 3260
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 1.48 46.62 42575 2427 99.9 0.1888 0.1871 0.2028 0.2175 0.2364 RANDOM 23.167
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] 2.01 -1.7 -0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.708 r_dihedral_angle_4_deg 16.988 r_dihedral_angle_3_deg 12.369 r_dihedral_angle_1_deg 6.855 r_mcangle_it 2.607 r_mcbond_it 1.825 r_mcbond_other 1.798 r_angle_refined_deg 1.658 r_angle_other_deg 1.402 r_chiral_restr 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.708 r_dihedral_angle_4_deg 16.988 r_dihedral_angle_3_deg 12.369 r_dihedral_angle_1_deg 6.855 r_mcangle_it 2.607 r_mcbond_it 1.825 r_mcbond_other 1.798 r_angle_refined_deg 1.658 r_angle_other_deg 1.402 r_chiral_restr 0.08 r_bond_refined_d 0.01 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 2198 Nucleic Acid Atoms Solvent Atoms 161 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing