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Crystal Structure Analysis of DesI in the presence of its TDP-sugar product
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OGA PDB entry 2OGA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 Sitting drop (batch) 8 293 7 mg/ml DesI, 75 mM NaCl, 150 mM LiCl, 14%PEG 8000, 10 mM dTDP-4-amino-4,6-dideoxy-alpha,D-glucose, 5 mM HEPES, 50 mM HEPPS, pH 8.0, Sitting drop (batch), temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.64 53.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.5 α = 90 b = 66.8 β = 90 c = 242 γ = 90
Symmetry Space Group P 21 21 21
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 Bruker Platinum 135 Montel 2007-02-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.08 50 94.9 0.057 0.057 16 4.4 59056 56057
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.08 2.18 73.4 0.35 0.35 2.4 2.9 7630
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB entry 2OGA 2.1 44.84 57438 55830 5599 97.2 0.184 0.184 0.18 0.1773 0.248 0.1796 random
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 t_angle_deg 2.27 t_bond_d 0.011 t_trig_c_planes 0.008 t_gen_planes 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5942 Nucleic Acid Atoms Solvent Atoms 593 Heterogen Atoms 100
Software Software Software Name Purpose PROTEUM PLUS data collection PHASER phasing TNT refinement SAINT data reduction SADABS data scaling