☰ Navigation Tabs
3-deoxy-D-arabino-heptulosonate 7-phosphate synthase from Mycobacterium tuberculosis in complex with D/L-tryptophan and D-phenylalanine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NV8 PDB entry 3NV8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS-HCL, PH 7.5, 1.5M AMMONIUM SULFATE, 12% V/V GLYCEROL. CRYSTALS WERE SOAKED IN THE SAME SOLUTION WITH AN ADDITIONAL 10% V/V GLYCEROL AND 0.25 MILLIM D-PHENYLALANINE AND 2.5 MILLIM TRYPTOPHAN
Crystal Properties Matthews coefficient Solvent content 4.05 69.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 206.357 α = 90 b = 206.357 β = 90 c = 66.941 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 315r 2012-10-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.953700 Australian Synchrotron MX2
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 2.33 47.55 100 4.2 12.3 71044
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 PDB entry 3NV8 2.4 47.55 60738 3128 99.9 0.138 0.137 0.1687 0.161 0.1868 RANDOM 35.17
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 -0.02 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.909 r_dihedral_angle_4_deg 18.09 r_dihedral_angle_3_deg 15.159 r_dihedral_angle_1_deg 6.542 r_angle_refined_deg 2.006 r_angle_other_deg 1.21 r_chiral_restr 0.108 r_bond_refined_d 0.019 r_gen_planes_refined 0.011 r_bond_other_d 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.909 r_dihedral_angle_4_deg 18.09 r_dihedral_angle_3_deg 15.159 r_dihedral_angle_1_deg 6.542 r_angle_refined_deg 2.006 r_angle_other_deg 1.21 r_chiral_restr 0.108 r_bond_refined_d 0.019 r_gen_planes_refined 0.011 r_bond_other_d 0.006 r_gen_planes_other 0.005 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7030 Nucleic Acid Atoms Solvent Atoms 131 Heterogen Atoms 112
Software Software Software Name Purpose REFMAC refinement Aimless data scaling MOLREP phasing PDB_EXTRACT data extraction XDS data reduction