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The structure of 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase from Mycobacterium tuberculosis complexed with phenylalanine and tryptophan
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2B7O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 20mM BTP, 150mM NaCl, 0.5mM TCEP, 0.005%(v/v) Thesit, 0.2mM PEP, 0.1mM MnCl2, 0.1M Na HEPES, 0.8M NaK phosphate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291.0K
Crystal Properties Matthews coefficient Solvent content 3.95 68.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 204.537 α = 90 b = 204.537 β = 90 c = 66.462 γ = 120
Symmetry Space Group P 32 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 120 IMAGE PLATE RIGAKU RAXIS IV Osmic Blue Mirrors 2005-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.542
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 39.5 98.2 0.064 8.2 2.07 105425 105425 37.5
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 2.07 87.2 0.381 2.1 2.38 10487
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 2b7o 2 32.67 105110 105110 5245 97.91 0.16423 0.164 0.163 0.1731 0.191 0.198 RANDOM 25.418
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] -0.15 -0.08 -0.15 0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.003 r_dihedral_angle_4_deg 15.749 r_dihedral_angle_3_deg 12.893 r_dihedral_angle_1_deg 6.187 r_scangle_it 4.212 r_scbond_it 2.796 r_angle_refined_deg 1.318 r_mcangle_it 1.09 r_angle_other_deg 0.976 r_mcbond_it 0.696
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.003 r_dihedral_angle_4_deg 15.749 r_dihedral_angle_3_deg 12.893 r_dihedral_angle_1_deg 6.187 r_scangle_it 4.212 r_scbond_it 2.796 r_angle_refined_deg 1.318 r_mcangle_it 1.09 r_angle_other_deg 0.976 r_mcbond_it 0.696 r_symmetry_vdw_other 0.269 r_nbd_refined 0.204 r_nbd_other 0.203 r_nbtor_refined 0.164 r_xyhbond_nbd_refined 0.163 r_symmetry_hbond_refined 0.163 r_mcbond_other 0.161 r_symmetry_vdw_refined 0.101 r_nbtor_other 0.083 r_chiral_restr 0.074 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d 0.004 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6976 Nucleic Acid Atoms Solvent Atoms 771 Heterogen Atoms 191
Software Software Software Name Purpose CrystalClear data collection CCP4 model building REFMAC refinement d*TREK data reduction d*TREK data scaling CCP4 phasing