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The Structure of 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase from Mycobacterium tuberculosis
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 291K
Crystal Properties Matthews coefficient Solvent content 3.9 68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 204.085 α = 90 b = 204.085 β = 90 c = 66.23 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 4 Double-crystal, Si(111) 2004-12-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 0.9796 ALS 5.0.2
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 2.3 50 100 0.124 23.9 11.2 70357 70357
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 2.3 2.38 100 0.652 3.9 10.4 6984
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 2.3 47.04 66796 66796 3563 100 0.18966 0.18966 0.18778 0.1869 0.22429 0.1888 RANDOM 43.524
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] 0.06 0.03 0.06 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.419 r_dihedral_angle_4_deg 19.552 r_dihedral_angle_3_deg 16.807 r_dihedral_angle_1_deg 6.495 r_scangle_it 4.294 r_scbond_it 2.906 r_mcangle_it 1.939 r_angle_refined_deg 1.667 r_mcbond_it 1.393 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.419 r_dihedral_angle_4_deg 19.552 r_dihedral_angle_3_deg 16.807 r_dihedral_angle_1_deg 6.495 r_scangle_it 4.294 r_scbond_it 2.906 r_mcangle_it 1.939 r_angle_refined_deg 1.667 r_mcbond_it 1.393 r_nbtor_refined 0.304 r_nbd_refined 0.224 r_symmetry_vdw_refined 0.208 r_xyhbond_nbd_refined 0.172 r_chiral_restr 0.138 r_symmetry_hbond_refined 0.108 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6936 Nucleic Acid Atoms Solvent Atoms 336 Heterogen Atoms 57
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling SHELXS phasing