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Crystal Structure of AlkB in complex with Fe(II), succinate, and methylated trinucleotide T-meA-T
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FD8 PDB 2FD8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 22-24% (w/v) PEG 3350, 10% glycerol and 200 mM sodium formate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.96 37.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.466 α = 90 b = 40.466 β = 90 c = 117.366 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV Yale/MSC mirrors 2005-08-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.54180
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 20 99 0.089 17.77 4.8 9504
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) 2.2 2.28 98.3 0.304 4.8 3.9 932
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (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 2FD8 2.2 19.94 1 9172 965 95.8 0.195 0.1932 0.231 0.2292 RANDOM 19.1
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] -2.02 -2.02 4.03
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 26.3 c_scangle_it 2.89 c_scbond_it 1.99 c_mcangle_it 1.91 c_angle_deg 1.6 c_improper_angle_d 1.51 c_mcbond_it 1.23 c_bond_d 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1556 Nucleic Acid Atoms 63 Solvent Atoms 119 Heterogen Atoms 9
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling CNS refinement PDB_EXTRACT data extraction COMO phasing