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Tryptophan Synthase from Salmonella typhimurium in complex with two molecules of N-(4'-trifluoromethoxybenzoyl)-2-amino-1-ethylphosphate (F6F) inhibitor in the alpha-site and a single F6F molecule in the beta-site at 1.54 Angstrom resolution.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4Y6G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.8 298 50 mM Bicine-NaOH, containing 10-14% PEG 8,000, and 2 mM spermine
Crystal Properties Matthews coefficient Solvent content 2.52 51.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 183.529 α = 90 b = 58.63 β = 94.92 c = 67.22 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 2015-04-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 12.3.1 0.97930 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 1.54 30 95 0.105 0.105 0.123 0.063 0.987 7.2 3.8 99870 99870
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 1.54 1.62 92.4 0.556 0.044 0.026 0.813 2.1 3.8 14139
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 4Y6G 1.54 29.31 94912 4955 94.77 0.1382 0.1357 0.1351 0.1866 0.1865 RANDOM 20.132
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] 0.19 -0.05 -0.33 0.15
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 39.105 r_dihedral_angle_2_deg 36.569 r_sphericity_bonded 19.13 r_dihedral_angle_4_deg 17.931 r_dihedral_angle_3_deg 12.066 r_dihedral_angle_1_deg 5.778 r_scbond_it 2.608 r_mcangle_it 2.456 r_rigid_bond_restr 2.371 r_mcbond_it 1.863
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 39.105 r_dihedral_angle_2_deg 36.569 r_sphericity_bonded 19.13 r_dihedral_angle_4_deg 17.931 r_dihedral_angle_3_deg 12.066 r_dihedral_angle_1_deg 5.778 r_scbond_it 2.608 r_mcangle_it 2.456 r_rigid_bond_restr 2.371 r_mcbond_it 1.863 r_angle_refined_deg 1.736 r_chiral_restr 0.114 r_bond_refined_d 0.016 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5018 Nucleic Acid Atoms Solvent Atoms 869 Heterogen Atoms 127
Software Software Software Name Purpose REFMAC refinement Blu-Ice data collection SCALA data scaling MOLREP phasing DM phasing PDB_EXTRACT data extraction iMOSFLM data reduction