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Crystal structure of a transketolase from Burkholderia thailandensis with an oxidized cysteinesulfonic acid in the active site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2R5N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 289 ButhA.01294.a.A1 PS01189 at 44.4 mg/mL against Emerald BioSystems Wizard III screen condition D6, 30% PEG 4000, 0.1 M Tris pH 8.5, 0.2 M lithium sulfate and 25% ethylene glycol as cryo-protectant, crystal tracking ID 225951d6, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.44 49.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 145.35 α = 90 b = 145.35 β = 90 c = 142.04 γ = 90
Symmetry Space Group P 41 21 2
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 MARMOSAIC 300 mm CCD 2011-10-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
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 2.15 50 99.2 0.076 16.08 7.1 82910 82278 -3 40.757
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 2.15 2.21 99.9 0.514 3.62
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 2r5n 2.15 50 82278 4121 99.23 0.1875 0.1855 0.225 0.2239 RANDOM 36.4024
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] -0.42 -0.42 0.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.539 r_dihedral_angle_4_deg 17.069 r_dihedral_angle_3_deg 14.524 r_dihedral_angle_1_deg 6.296 r_angle_refined_deg 1.489 r_chiral_restr 0.099 r_bond_refined_d 0.012 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9879 Nucleic Acid Atoms Solvent Atoms 642 Heterogen Atoms 11
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction