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Crystal structure of human NEIL1(P2G, E3Q, K242) bound to duplex DNA containing spiroiminodihydantoin (Sp)
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 2.77 55.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.757 α = 90 b = 143.614 β = 90 c = 71.251 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 2017-04-23 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 2.91 50 99.3 0.08 0.089 0.037 14.2 5.8 20492
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 2.91 2.96 100 0.96 1.052 0.427 0.885 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 2.91 37.7 19472 983 98.65 0.193 0.1906 0.1912 0.2429 0.2394 RANDOM 115.328
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] -7.09 4.39 2.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.982 r_dihedral_angle_4_deg 19.085 r_dihedral_angle_3_deg 18.093 r_dihedral_angle_1_deg 13.152 r_angle_refined_deg 1.78 r_angle_other_deg 1.337 r_chiral_restr 0.077 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_gen_planes_other 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.982 r_dihedral_angle_4_deg 19.085 r_dihedral_angle_3_deg 18.093 r_dihedral_angle_1_deg 13.152 r_angle_refined_deg 1.78 r_angle_other_deg 1.337 r_chiral_restr 0.077 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4121 Nucleic Acid Atoms 1058 Solvent Atoms 55 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction SCALEPACK data scaling PHASER phasing