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Crystal structure of Tryptophan Synthase from Salmonella typhimurium in complex with F9 ligand in the alpha-site and the product L-Tryptophan in the beta-site.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4HT3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.6 298 50 mM Bicine-CsOH, pH 7.6, 10% PEG 8,000, 100 mM CsCl2, 1 mM spermine
Crystal Properties Matthews coefficient Solvent content 2.54 51.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 182.553 α = 90 b = 59.3 β = 94.82 c = 67.368 γ = 90
Symmetry Space Group C 1 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 2012-05-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 12.3.1 1.0000 ALS 12.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) 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 1.18 40 98.6 0.081 0.081 0.086 0.028 0.999 14.7 9.3 231646 231646
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.18 1.24 94.2 0.872 0.037 0.015 0.778 3 7.9 32187
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 4HT3 1.18 39.21 219965 11610 98.52 0.1414 0.1404 0.1395 0.1605 0.1597 RANDOM 17.768
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] 0.08 0.44 -0.29 0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.27 r_sphericity_free 18.535 r_dihedral_angle_4_deg 16.187 r_dihedral_angle_3_deg 11.607 r_sphericity_bonded 10.796 r_rigid_bond_restr 10.73 r_dihedral_angle_1_deg 5.81 r_scbond_it 1.784 r_mcangle_it 1.437 r_angle_refined_deg 1.406
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.27 r_sphericity_free 18.535 r_dihedral_angle_4_deg 16.187 r_dihedral_angle_3_deg 11.607 r_sphericity_bonded 10.796 r_rigid_bond_restr 10.73 r_dihedral_angle_1_deg 5.81 r_scbond_it 1.784 r_mcangle_it 1.437 r_angle_refined_deg 1.406 r_mcbond_it 1.186 r_chiral_restr 0.092 r_bond_refined_d 0.012 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4971 Nucleic Acid Atoms Solvent Atoms 825 Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing DM phasing PDB_EXTRACT data extraction