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PanDDA analysis group deposition -- Crystal Structure of human NUDT22 in complex with N08253b
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 38.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.56 α = 90 b = 52.35 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 2016-07-02 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 1.44 50.8 99.9 0.052 0.057 0.022 1 17.2 6.4 48674
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 1.44 1.48 99.9 1.535 1.693 0.708 0.474 5.6 3544
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 1.44 50.8 45996 2610 99.86 0.1888 0.1869 0.2059 0.219 0.2373 RANDOM 23.309
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] 1.71 -1.53 -0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.524 r_dihedral_angle_4_deg 17.91 r_dihedral_angle_3_deg 12.371 r_dihedral_angle_1_deg 6.903 r_mcangle_it 2.645 r_mcbond_it 1.793 r_mcbond_other 1.77 r_angle_refined_deg 1.696 r_angle_other_deg 1.419 r_chiral_restr 0.085
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.524 r_dihedral_angle_4_deg 17.91 r_dihedral_angle_3_deg 12.371 r_dihedral_angle_1_deg 6.903 r_mcangle_it 2.645 r_mcbond_it 1.793 r_mcbond_other 1.77 r_angle_refined_deg 1.696 r_angle_other_deg 1.419 r_chiral_restr 0.085 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 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 161 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing