☰ Navigation Tabs
Crystal structure of human NEIL1(P2G, E3Q, K242) bound to duplex DNA containing 5-hydroxyuracil (5-OHU)
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 2.76 55.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.559 α = 90 b = 109.771 β = 90 c = 169.173 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 2015-11-15 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 2.75 50 100 0.138 0.151 0.06 5.2 6.4 35964
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 2.75 2.8 100 0.78 0.855 0.347 0.837 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 2.76 49.58 34141 1765 99.51 0.2095 0.2075 0.209 0.2459 0.2472 RANDOM 81.026
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] -1.86 -4.11 5.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.112 r_dihedral_angle_4_deg 22.323 r_dihedral_angle_3_deg 17.529 r_dihedral_angle_1_deg 11.657 r_angle_refined_deg 1.627 r_angle_other_deg 1.351 r_chiral_restr 0.079 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_gen_planes_other 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.112 r_dihedral_angle_4_deg 22.323 r_dihedral_angle_3_deg 17.529 r_dihedral_angle_1_deg 11.657 r_angle_refined_deg 1.627 r_angle_other_deg 1.351 r_chiral_restr 0.079 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_gen_planes_other 0.004 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5791 Nucleic Acid Atoms 1575 Solvent Atoms 138 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction SCALEPACK data scaling PHASER phasing