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X-ray structure of AlkB protein bound to dsDNA containing 1meA/A with cofactors
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 2.51 50.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.407 α = 90 b = 75.629 β = 107.73 c = 50.972 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 2007-11-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C 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 1.8 50 89.7 0.093 10 3.2 24645 24645
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 1.8 1.86 69.8 0.25 3.6 3.1
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 1.9 20 20726 1114 92.53 0.21634 0.21462 0.2145 0.24714 0.2431 RANDOM 32.669
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] -2.14 -0.08 -2.55 4.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.257 r_dihedral_angle_4_deg 15.316 r_dihedral_angle_3_deg 12.089 r_dihedral_angle_1_deg 5.651 r_scangle_it 1.15 r_angle_refined_deg 1.093 r_scbond_it 0.643 r_mcangle_it 0.459 r_nbtor_refined 0.299 r_mcbond_it 0.279
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.257 r_dihedral_angle_4_deg 15.316 r_dihedral_angle_3_deg 12.089 r_dihedral_angle_1_deg 5.651 r_scangle_it 1.15 r_angle_refined_deg 1.093 r_scbond_it 0.643 r_mcangle_it 0.459 r_nbtor_refined 0.299 r_mcbond_it 0.279 r_nbd_refined 0.175 r_symmetry_hbond_refined 0.106 r_xyhbond_nbd_refined 0.097 r_symmetry_vdw_refined 0.09 r_chiral_restr 0.061 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 1572 Nucleic Acid Atoms 515 Solvent Atoms 168 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement ADSC data collection HKL-2000 data reduction HKL-2000 data scaling PHASES phasing