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PanDDA analysis group deposition -- Crystal Structure of human NUDT22 in complex with N13441a
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 38.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.66 α = 90 b = 52.18 β = 90 c = 101.76 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 2.11 52.18 99.8 0.183 0.2 0.078 0.996 8.8 6.4 15832
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 2.11 2.16 100 1.385 1.508 0.59 0.515 6.4 1162
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 2.11 50.88 14909 877 99.76 0.1964 0.1918 0.2065 0.2697 0.2734 RANDOM 35.992
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] 2.74 -3.58 0.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.752 r_dihedral_angle_4_deg 19.352 r_dihedral_angle_3_deg 14.852 r_dihedral_angle_1_deg 6.891 r_mcangle_it 3.755 r_mcbond_it 2.578 r_mcbond_other 2.573 r_angle_refined_deg 1.541 r_angle_other_deg 1.246 r_chiral_restr 0.072
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.752 r_dihedral_angle_4_deg 19.352 r_dihedral_angle_3_deg 14.852 r_dihedral_angle_1_deg 6.891 r_mcangle_it 3.755 r_mcbond_it 2.578 r_mcbond_other 2.573 r_angle_refined_deg 1.541 r_angle_other_deg 1.246 r_chiral_restr 0.072 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2198 Nucleic Acid Atoms Solvent Atoms 154 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing