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Iron-Catalyzed Oxidation Intermediates Captured in A DNA Repair Dioxygenase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BIE PDB entry 3BIE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 20% (w/v) PEG 8K, 100 mM Sodium Chloride, 25 mM magnesium chloride, 0.1M cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.48 50.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.44 α = 90 b = 75.95 β = 107.76 c = 51.17 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 277 CCD MAR CCD 130 mm 2008-10-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C 0.9266 APS 14-BM-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.55 50 99.6 0.041 19.2 3.5 47998 47806 2.1 2.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.55 99.6 0.368 2.1 3.4 4763
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) 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 3BIE 1.75 20 6 6 28902 28324 1531 98 0.1673 0.16725 0.16599 0.1681 0.19073 0.192 RANDOM 9.917
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] -0.43 -0.11 -0.38 0.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.786 r_dihedral_angle_4_deg 13.048 r_dihedral_angle_3_deg 10.796 r_dihedral_angle_1_deg 5.578 r_scangle_it 2.142 r_scbond_it 1.342 r_angle_refined_deg 1.18 r_mcangle_it 0.93 r_mcbond_it 0.499 r_chiral_restr 0.073
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.786 r_dihedral_angle_4_deg 13.048 r_dihedral_angle_3_deg 10.796 r_dihedral_angle_1_deg 5.578 r_scangle_it 2.142 r_scbond_it 1.342 r_angle_refined_deg 1.18 r_mcangle_it 0.93 r_mcbond_it 0.499 r_chiral_restr 0.073 r_bond_refined_d 0.006 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1571 Nucleic Acid Atoms 501 Solvent Atoms 329 Heterogen Atoms 11
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling