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Crystal Structure of Escherichia coli AlkB in complex with ssDNA containing a 1-methylguanine lesion
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FD8 PDB ENTRY 2FD8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 288 10-20% PEG 8000, 0.1M MES, 0.1M sodium chloride, 0.1M magnesium chloride, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 288K
Crystal Properties Matthews coefficient Solvent content 2.15 42.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 147.809 α = 90 b = 41.441 β = 120.98 c = 85.622 γ = 90
Symmetry Space Group C 1 2 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 RIGAKU SATURN 92 2009-05-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.54
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 2.2 42.69 99.6 0.104 9.4 6.94 22909 21726
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 2.2 2.23 99.94 0.396 9.4 6.27 1661
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 PDB ENTRY 2FD8 2.2 23.74 21726 1156 99.68 0.21434 0.21126 0.27326 0.2481 RANDOM 18.165
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] -0.19 0.15 -0.13 0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.975 r_dihedral_angle_4_deg 17.682 r_dihedral_angle_3_deg 16.879 r_dihedral_angle_1_deg 6.632 r_scangle_it 1.998 r_angle_refined_deg 1.619 r_scbond_it 1.191 r_mcangle_it 0.734 r_mcbond_it 0.396 r_chiral_restr 0.087
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.975 r_dihedral_angle_4_deg 17.682 r_dihedral_angle_3_deg 16.879 r_dihedral_angle_1_deg 6.632 r_scangle_it 1.998 r_angle_refined_deg 1.619 r_scbond_it 1.191 r_mcangle_it 0.734 r_mcbond_it 0.396 r_chiral_restr 0.087 r_bond_refined_d 0.009 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3243 Nucleic Acid Atoms 246 Solvent Atoms 269 Heterogen Atoms 22
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement d*TREK data reduction d*TREK data scaling