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Crystal Structure Complex Between the Lactococcus Lactis FPG (Mutm) and a FAPY-dG Containing DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NNJ PDB ENTRY 1NNJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 hepes, sodium citrate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.37 63.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.408 α = 90 b = 91.408 β = 90 c = 141.575 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 4 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.9330 ESRF ID14-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.8 76.7 99.3 0.048 8.7 3.6 55781 55781 24.879
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.9 100 0.234 3.1 3.6 8083
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1NNJ 1.8 20 52844 52844 2825 99.07 0.18034 0.18034 0.17891 0.1916 0.20697 0.213 RANDOM 28.788
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] -0.02 -0.02 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.737 r_scangle_it 4.122 r_scbond_it 2.62 r_mcangle_it 1.755 r_angle_refined_deg 1.709 r_mcbond_it 0.989 r_nbd_refined 0.21 r_symmetry_hbond_refined 0.178 r_xyhbond_nbd_refined 0.143 r_symmetry_vdw_refined 0.131
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.737 r_scangle_it 4.122 r_scbond_it 2.62 r_mcangle_it 1.755 r_angle_refined_deg 1.709 r_mcbond_it 0.989 r_nbd_refined 0.21 r_symmetry_hbond_refined 0.178 r_xyhbond_nbd_refined 0.143 r_symmetry_vdw_refined 0.131 r_chiral_restr 0.109 r_bond_refined_d 0.018 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2110 Nucleic Acid Atoms 569 Solvent Atoms 431 Heterogen Atoms 7
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling AMoRE phasing REFMAC refinement CCP4 data scaling