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Crystal structure of human NEIL1(R242, Y244R) bound to duplex DNA containing 2'-fluoro-2'-deoxy-5,6-dihydrouridine
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 2.82 56.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.938 α = 90 b = 109.635 β = 90 c = 171.944 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 CCD MAR CCD 130 mm 2017-05-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.9793 SSRF BL17U1
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 2.64 50 99.7 0.09 0.101 0.044 11 5 41670
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 2.64 2.69 100 0.992 1.099 0.468 0.715 5.2
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 2.64 36.17 39478 2130 99.41 0.2049 0.2034 0.2041 0.2319 0.2303 RANDOM 81.84
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] -1.55 0.34 1.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.928 r_dihedral_angle_4_deg 21.952 r_dihedral_angle_3_deg 17.791 r_dihedral_angle_1_deg 10.903 r_angle_refined_deg 1.61 r_angle_other_deg 1.333 r_chiral_restr 0.081 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.928 r_dihedral_angle_4_deg 21.952 r_dihedral_angle_3_deg 17.791 r_dihedral_angle_1_deg 10.903 r_angle_refined_deg 1.61 r_angle_other_deg 1.333 r_chiral_restr 0.081 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5876 Nucleic Acid Atoms 1575 Solvent Atoms 216 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction SCALEPACK data scaling PHASER phasing