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The structure of 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase from mycobacterium tuberculosis complexed with 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 7.5 295 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 295K
Crystal Properties Matthews coefficient Solvent content 3.94 68.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 204.712 α = 90 b = 204.712 β = 90 c = 66.264 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 100 CCD ADSC QUANTUM 315 Double-crystal, Si(111) 2005-03-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.97929 SSRL BL9-2
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 2.5 50 100 0.134 10.4 2.8 52344 52344
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 2.5 2.59 100 0.633 2.1 2.8 52344
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2B7O 2.5 38.69 52324 2815 99.98 0.19101 0.18901 0.1881 0.22814 0.2265 RANDOM 28.181
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] -0.02 -0.01 -0.02 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.629 r_dihedral_angle_4_deg 21.011 r_dihedral_angle_3_deg 17.228 r_dihedral_angle_1_deg 6.698 r_scangle_it 4.766 r_scbond_it 3.239 r_mcangle_it 2.144 r_angle_refined_deg 1.67 r_angle_other_deg 1.305 r_mcbond_it 1.249
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.629 r_dihedral_angle_4_deg 21.011 r_dihedral_angle_3_deg 17.228 r_dihedral_angle_1_deg 6.698 r_scangle_it 4.766 r_scbond_it 3.239 r_mcangle_it 2.144 r_angle_refined_deg 1.67 r_angle_other_deg 1.305 r_mcbond_it 1.249 r_mcbond_other 0.435 r_chiral_restr 0.093 r_bond_refined_d 0.018 r_gen_planes_refined 0.014 r_gen_planes_other 0.013 r_bond_other_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6871 Nucleic Acid Atoms Solvent Atoms 297 Heterogen Atoms 121
Software Software Software Name Purpose Blu-Ice data collection CCP4 model building REFMAC refinement DENZO data reduction SCALEPACK data scaling CCP4 phasing