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Crystal structure of human NEIL1(R242) bound to duplex DNA containing a C:T mismatch
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 2.81 56.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.075 α = 90 b = 109.23 β = 90 c = 171.985 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 2014-12-02 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 2.88 50 97.7 0.109 0.118 0.056 9 4.5 31227
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.88 2.93 97 0.99 0.498 0.49 4.6
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 2.89 43.03 29662 1529 97.46 0.2394 0.2372 0.2371 0.2828 0.2832 RANDOM 80.78
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] 0.26 -1.1 0.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.74 r_dihedral_angle_4_deg 21.404 r_dihedral_angle_3_deg 17.506 r_dihedral_angle_1_deg 11.084 r_angle_refined_deg 1.64 r_angle_other_deg 1.362 r_chiral_restr 0.08 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.74 r_dihedral_angle_4_deg 21.404 r_dihedral_angle_3_deg 17.506 r_dihedral_angle_1_deg 11.084 r_angle_refined_deg 1.64 r_angle_other_deg 1.362 r_chiral_restr 0.08 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.004 r_gen_planes_other 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5848 Nucleic Acid Atoms 1575 Solvent Atoms 98 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction SCALEPACK data scaling PHASER phasing