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Crystal structure of a complex between the wild-type lactococcus lactis Fpg (MutM) and a N7-Benzyl-Fapy-dG containing DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XC8 PDB ENTRY 1XC8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 HEPES, Sodium citrate, PH7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
Crystal Properties Matthews coefficient Solvent content 3.67 66.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.356 α = 90 b = 91.356 β = 90 c = 140.943 γ = 90
Symmetry Space Group P 41 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 CCD ADSC QUANTUM 315 2006-03-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.97935 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 1.9 47.62 100 0.099 0.099 17 7 47718 47718 23.67
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 2 100 0.451 0.451 3.3 7.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1XC8 1.9 45.69 45259 45259 2411 100 0.173 0.173 0.172 0.2 0.1894 RANDOM
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.775 r_dihedral_angle_4_deg 19.997 r_dihedral_angle_3_deg 12.291 r_dihedral_angle_1_deg 5.825 r_scangle_it 3.769 r_scbond_it 2.602 r_angle_refined_deg 1.745 r_mcangle_it 1.621 r_mcbond_it 1.114 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.775 r_dihedral_angle_4_deg 19.997 r_dihedral_angle_3_deg 12.291 r_dihedral_angle_1_deg 5.825 r_scangle_it 3.769 r_scbond_it 2.602 r_angle_refined_deg 1.745 r_mcangle_it 1.621 r_mcbond_it 1.114 r_nbtor_refined 0.306 r_nbd_refined 0.217 r_symmetry_vdw_refined 0.18 r_xyhbond_nbd_refined 0.159 r_symmetry_hbond_refined 0.14 r_bond_refined_d 0.018 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2126 Nucleic Acid Atoms 576 Solvent Atoms 335 Heterogen Atoms 7
Software Software Software Name Purpose AMoRE phasing REFMAC refinement DNA data collection MOSFLM data reduction SCALA data scaling