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Crystal structure of human NEIL1(P2G, E3Q, K242) bound to duplex DNA containing guanidinohydantoin (Gh)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5ITY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277.15 0.1 M cacodylic acid (pH 6.5), 0.1 M NaCl, 0.05 M MgCl2 and 18% (w/v) PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.74 55.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.604 α = 90 b = 142.564 β = 90 c = 71.074 γ = 90
Symmetry Space Group P 21 21 2
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 2017-01-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.9793 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.79 50 99.5 0.075 0.082 0.033 13.2 6.1 22914
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 2.79 2.84 100 0.999 1.091 0.433 0.868 6.4
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 MOLECULAR REPLACEMENT THROUGHOUT 5ITY 2.79 37.62 21772 1106 99.37 0.1884 0.1856 0.1884 0.2433 0.24 RANDOM 106.906
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] -6.07 2.67 3.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.873 r_dihedral_angle_4_deg 19.784 r_dihedral_angle_3_deg 17.92 r_dihedral_angle_1_deg 13.7 r_angle_refined_deg 1.701 r_angle_other_deg 1.319 r_chiral_restr 0.074 r_gen_planes_refined 0.009 r_bond_refined_d 0.008 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.873 r_dihedral_angle_4_deg 19.784 r_dihedral_angle_3_deg 17.92 r_dihedral_angle_1_deg 13.7 r_angle_refined_deg 1.701 r_angle_other_deg 1.319 r_chiral_restr 0.074 r_gen_planes_refined 0.009 r_bond_refined_d 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4152 Nucleic Acid Atoms 1054 Solvent Atoms 65 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction SCALEPACK data scaling PHASER phasing