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Crystal structure of mycobacterium tuberculosis Transketolase (Rv1449c)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2R8O model of Rv1449c with E. coli transketolase (pdb entry 2r8o) as template
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293.15 17% PEG 10000, 0.1M ammonium acetate in 0.1M bis-tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
Crystal Properties Matthews coefficient Solvent content 2.32 46.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.53 α = 82.2 b = 80.12 β = 81.16 c = 130.1 γ = 66.37
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 225 mm CCD 2009-10-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 0.979 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.494 128.12 96.62 91429
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) 1 2.49 2.64 91.16 0.59 0.431 2.77 3.9 13701
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT model of Rv1449c with E. coli transketolase (pdb entry 2r8o) as template 2.49 19.81 2.01 91429 86846 4579 96.69 0.22544 0.22298 0.2268 0.2721 0.2732 RANDOM 27.069
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] 0.91 0.21 -1.64 1 -0.24 -1.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.555 r_dihedral_angle_4_deg 22.458 r_dihedral_angle_3_deg 17.625 r_dihedral_angle_1_deg 6.235 r_scangle_it 2.603 r_angle_refined_deg 1.634 r_scbond_it 1.572 r_mcangle_it 1.064 r_mcbond_it 0.566 r_chiral_restr 0.097
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.555 r_dihedral_angle_4_deg 22.458 r_dihedral_angle_3_deg 17.625 r_dihedral_angle_1_deg 6.235 r_scangle_it 2.603 r_angle_refined_deg 1.634 r_scbond_it 1.572 r_mcangle_it 1.064 r_mcbond_it 0.566 r_chiral_restr 0.097 r_bond_refined_d 0.017 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 21150 Nucleic Acid Atoms Solvent Atoms 410 Heterogen Atoms 156
Software Software Software Name Purpose XDS data scaling PHASER phasing REFMAC refinement XDS data reduction