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X-ray structure of E coli AlkB bound to dsDNA containing 1meA/T with Mn and 2KG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 24w/v% PEG 8000, 100mM sodium chloride, 50mM magnesium chloride, 0.1M cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.58 52.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.413 α = 90 b = 75.822 β = 108.53 c = 52.228 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 1.62 50 88.8 0.082 17 5.5 34683 34683
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 1.62 1.68 56.6 0.344 2.87 4.4 2207
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.68 20 30668 1624 92.6 0.18783 0.18657 0.1863 0.21082 0.21 RANDOM 24.991
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] -1.39 0.09 -1.19 2.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.14 r_dihedral_angle_4_deg 12.316 r_dihedral_angle_3_deg 12.284 r_dihedral_angle_1_deg 5.562 r_angle_refined_deg 1.099 r_scangle_it 1.033 r_scbond_it 0.648 r_mcangle_it 0.538 r_mcbond_it 0.35 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.14 r_dihedral_angle_4_deg 12.316 r_dihedral_angle_3_deg 12.284 r_dihedral_angle_1_deg 5.562 r_angle_refined_deg 1.099 r_scangle_it 1.033 r_scbond_it 0.648 r_mcangle_it 0.538 r_mcbond_it 0.35 r_nbtor_refined 0.3 r_nbd_refined 0.174 r_xyhbond_nbd_refined 0.089 r_symmetry_vdw_refined 0.08 r_chiral_restr 0.062 r_symmetry_hbond_refined 0.055 r_bond_refined_d 0.006 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 1581 Nucleic Acid Atoms 505 Solvent Atoms 259 Heterogen Atoms 11
Software Software Software Name Purpose PHASES phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling