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Crystal structure of Tryptophan Synthase from Salmonella typhimurium in complex with two F6F molecules in the alpha-site and one F6F molecule in the beta-site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4KKX PDB entry 4KKX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.8 298 50 mM Bicine-NaOH, pH 7.8; 10% PEG 8,000; 2 mM spermine
Crystal Properties Matthews coefficient Solvent content 2.53 51.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 183.809 α = 90 b = 58.89 β = 95.21 c = 67.27 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 IMAGE PLATE RIGAKU RAXIS IV++ 2013-03-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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 1.75 20.95 99.9 0.07 9.9 3.5 72402 72402 21.5
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 1.75 1.84 100 0.461 2.1 3.4
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 4KKX 1.75 20.95 72402 3601 99.89 0.1603 0.1584 0.1704 0.1885 0.197 RANDOM 26.729
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] -0.31 0.04 0.1 0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.516 r_dihedral_angle_4_deg 18.697 r_dihedral_angle_3_deg 12.696 r_dihedral_angle_1_deg 5.764 r_mcangle_it 2.284 r_angle_refined_deg 1.721 r_mcbond_it 1.484 r_mcbond_other 1.473 r_angle_other_deg 0.872 r_chiral_restr 0.105
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.516 r_dihedral_angle_4_deg 18.697 r_dihedral_angle_3_deg 12.696 r_dihedral_angle_1_deg 5.764 r_mcangle_it 2.284 r_angle_refined_deg 1.721 r_mcbond_it 1.484 r_mcbond_other 1.473 r_angle_other_deg 0.872 r_chiral_restr 0.105 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4905 Nucleic Acid Atoms Solvent Atoms 617 Heterogen Atoms 90
Software Software Software Name Purpose PDB_EXTRACT data extraction REFMAC refinement MOLREP phasing SCALA data scaling iMOSFLM data reduction CrystalClear data collection d*TREK data reduction SCALEPACK data scaling