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X-ray structure of E coli AlkB crosslinked to dsDNA in the active site
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 20% PEG 5000, 0.1M sodium chloride, 25 mM magnesium chloride, 0.1M cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.33 47.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.397 α = 90 b = 75.507 β = 105.45 c = 46.788 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 100 CCD ADSC QUANTUM 315 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-D 0.97 APS 14-BM-D
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 1.59 50 98.6 0.059 16 3.7 36607 36607
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 1.59 1.65 87.3 0.366 2 2.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) 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 1.65 20 31663 1663 99.86 0.18882 0.18756 0.21236 0.2748 RANDOM 22.876
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] -0.69 -0.13 -0.4 1.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.848 r_dihedral_angle_3_deg 11.434 r_dihedral_angle_4_deg 11.354 r_dihedral_angle_1_deg 5.764 r_angle_refined_deg 1.04 r_scangle_it 0.984 r_scbond_it 0.618 r_mcangle_it 0.53 r_mcbond_it 0.365 r_nbtor_refined 0.297
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.848 r_dihedral_angle_3_deg 11.434 r_dihedral_angle_4_deg 11.354 r_dihedral_angle_1_deg 5.764 r_angle_refined_deg 1.04 r_scangle_it 0.984 r_scbond_it 0.618 r_mcangle_it 0.53 r_mcbond_it 0.365 r_nbtor_refined 0.297 r_nbd_refined 0.172 r_symmetry_vdw_refined 0.099 r_xyhbond_nbd_refined 0.094 r_symmetry_hbond_refined 0.063 r_chiral_restr 0.061 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1570 Nucleic Acid Atoms 529 Solvent Atoms 292 Heterogen Atoms 11
Software Software Software Name Purpose PHASES phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling