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The structure of 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase from mycobacterium tuberculosis cocrystallized and complexed with phenylalanine and tryptophan
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2B7O 2B7O, 3KGF experimental model PDB 3KGF 2B7O, 3KGF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 20MM BTP, 150MM NACL, 0.5MM TCEP, 0.2MM PEP, 0.1MM MNCL2, 0.1M HEPES, 0.8M NAK PHOSPHATE, pH 8.0, 0.1MM Trp and Phe ligands, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal Properties Matthews coefficient Solvent content 4.11 70.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 207.56 α = 90 b = 207.56 β = 90 c = 66.977 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 123 IMAGE PLATE RIGAKU RAXIS IV++ AXCo PX70 capillary optic 2010-03-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
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 1.95 31.88 99.2 0.084 8.7 3.96 119335
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 1.95 2.02 95.5 0.442 2.3 2.98 11440
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 (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, 3KGF 1.95 31.88 113806 6034 99.49 0.1536 0.1536 0.1529 0.154 0.168 0.1704 RANDOM 33.9347
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] -0.29 -0.29 0.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.851 r_dihedral_angle_4_deg 18.167 r_dihedral_angle_3_deg 14.921 r_dihedral_angle_1_deg 7.86 r_scangle_it 6.053 r_scbond_it 4.512 r_mcangle_it 2.855 r_angle_other_deg 2.027 r_mcbond_it 1.998 r_angle_refined_deg 1.962
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.851 r_dihedral_angle_4_deg 18.167 r_dihedral_angle_3_deg 14.921 r_dihedral_angle_1_deg 7.86 r_scangle_it 6.053 r_scbond_it 4.512 r_mcangle_it 2.855 r_angle_other_deg 2.027 r_mcbond_it 1.998 r_angle_refined_deg 1.962 r_mcbond_other 0.506 r_chiral_restr 0.131 r_gen_planes_refined 0.017 r_bond_refined_d 0.016 r_gen_planes_other 0.012 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7011 Nucleic Acid Atoms Solvent Atoms 495 Heterogen Atoms 136
Software Software Software Name Purpose d*TREK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection d*TREK data reduction