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3-Deoxy-D-arabino-heptulosonate 7-phosphate synthase from Mycobacterium tuberculosis with D-tyrosine bound in the phenylalanine binding site
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 7.5 298 0.1 M Tris-HCl, pH 7.5, 1.5 M ammonium sulfate, 12% v/v glycerol. For soaking, 0.2 microliters of a 10 mM D-Tyr stock solution was added to equilibrated 2 microliter droplets at 48 hours and 24 hours before crystal freezing, respectively
Crystal Properties Matthews coefficient Solvent content 4 69.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 205.451 α = 90 b = 205.451 β = 90 c = 66.803 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 210r 2012-07-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.9537 Australian Synchrotron MX1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 2.05 19.85 99.9 0.143 0.056 0.997 11.8 7.5 101083
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.09 100 1.026 0.398 0.608 2.1 7.5 5007
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 3NV8 2.05 19.85 96017 5046 99.86 0.1948 0.1941 0.207 0.1816 RANDOM 27.469
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] 2.44 2.44 -4.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.373 r_dihedral_angle_4_deg 15.924 r_dihedral_angle_3_deg 12.761 r_dihedral_angle_1_deg 5.242 r_mcangle_it 2.339 r_mcbond_it 1.279 r_mcbond_other 1.279 r_angle_refined_deg 1.155 r_angle_other_deg 0.806 r_chiral_restr 0.061
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.373 r_dihedral_angle_4_deg 15.924 r_dihedral_angle_3_deg 12.761 r_dihedral_angle_1_deg 5.242 r_mcangle_it 2.339 r_mcbond_it 1.279 r_mcbond_other 1.279 r_angle_refined_deg 1.155 r_angle_other_deg 0.806 r_chiral_restr 0.061 r_gen_planes_refined 0.009 r_bond_refined_d 0.006 r_bond_other_d 0.005 r_gen_planes_other 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7045 Nucleic Acid Atoms Solvent Atoms 537 Heterogen Atoms 54
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction MOLREP phasing