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Crystal Structure of AlkB T208A mutant protein in complex with Co(II), 2-oxoglutarate, and methylated trinucleotide T-meA-T
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FD8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 22-24% (w/v) PEG3350, 10% glycerol, 200 mM sodium formate
Crystal Properties Matthews coefficient Solvent content 2.04 39.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.373 α = 90 b = 41.373 β = 90 c = 116.569 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 2008-08-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4A 0.97904 NSLS X4A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.33 30 98.8 0.048 0.053 0.023 17.4 5.6 44362 8.92
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.33 1.35 80.3 0.176 0.195 0.084 0.972 5.3 1775
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-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2FD8 1.333 29.255 1.38 44312 2202 99.68 0.1192 0.1178 0.1184 0.1472 0.1466 14.3926
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.477 f_angle_d 1.16 f_chiral_restr 0.078 f_bond_d 0.006 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1559 Nucleic Acid Atoms 63 Solvent Atoms 250 Heterogen Atoms 74
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction Coot model building HKL-2000 data scaling HKL-2000 data reduction COMO phasing