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Crystal Structure of AlkB in complex with Fe(II), 2-oxoglutarate, and methylated trinucleotide T-meA-T (air 3 hours)
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 1.99 38.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.646 α = 90 b = 40.656 β = 90 c = 117.924 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 CCD ADSC QUANTUM 4 mirrors 2005-09-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4A 0.97949 NSLS X4A
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 20 99.2 0.102 20.93 7.9 17611
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 97.8 0.636 2.15 5.2 1748
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 1.8 19.21 1 16614 1731 93.9 0.195 0.1947 0.226 0.2285 RANDOM 22.1
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] -0.76 -1.09 1.86
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 25.3 c_scangle_it 2.97 c_mcangle_it 2.04 c_scbond_it 1.98 c_mcbond_it 1.31 c_angle_deg 1.2 c_improper_angle_d 0.96 c_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1556 Nucleic Acid Atoms 63 Solvent Atoms 105 Heterogen Atoms 19
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling CNS refinement PDB_EXTRACT data extraction COMO phasing