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Tryptophan Synthase from Salmonella typhimurium in complex with a single molecule of 2-({[4-(trifluoromethoxy)phenyl]carbonyl}amino)ethyl dihydrogen phosphate (F6) in the alpha-site.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4WX2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.8 298 50mM Bicine-NaOH, pH 7.8, containing 50mM NaCl, 2mM spermine, and 10% PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.52 51.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 183.03 α = 90 b = 58.9 β = 94.91 c = 67.23 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++ VariMax 2013-03-01 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) 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 1.82 20 72.8 0.043 0.043 0.056 0.035 0.999 13.1 2.1 46573 46573
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 1.82 1.92 69.7 0.454 0.018 0.014 0.756 2 2.1 6445
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 4WX2 1.82 19.83 44334 2237 72.58 0.1705 0.1682 0.1679 0.2143 0.2139 RANDOM 25.879
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] -0.04 -0.03 0.05 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.417 r_dihedral_angle_4_deg 18.657 r_dihedral_angle_3_deg 14.47 r_dihedral_angle_1_deg 6.187 r_angle_refined_deg 1.655 r_mcangle_it 1.238 r_scbond_it 0.875 r_mcbond_it 0.705 r_chiral_restr 0.108 r_bond_refined_d 0.014
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.417 r_dihedral_angle_4_deg 18.657 r_dihedral_angle_3_deg 14.47 r_dihedral_angle_1_deg 6.187 r_angle_refined_deg 1.655 r_mcangle_it 1.238 r_scbond_it 0.875 r_mcbond_it 0.705 r_chiral_restr 0.108 r_bond_refined_d 0.014 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4924 Nucleic Acid Atoms Solvent Atoms 673 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing PDB_EXTRACT data extraction