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The external aldimine crystal structure of Salmonella typhimurium Tryptophan Synthase mutant beta-S377A in complex F9 inhibitor at the alpha-site and cesium ion at the metal coordination site. The single beta-Q114 rotamer conformation allows a hydrogen bond to form with the PLP oxygen at the position 3 in the ring
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6SXY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.8 298 50 mM Bicine-CsOH, 10% PEG 8,000, 4 mM Spermine, pH 7.8
Crystal Properties Matthews coefficient Solvent content 2.45 49.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 180.749 α = 90 b = 57.85 β = 94.54 c = 67.11 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++ Osmic Varimax HF ArcSec 2020-01-11 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 Sym I (Observed) Rrim I (All) Rpim I (All) 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 1.64 90.091 92.3 0.074 0.1 0.053 7.3 3.4 78381 78381
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.64 1.73 87.3 0.309 0.309 0.44 0.233 2.1 3.3
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 6SXY 1.64 38.82 74222 3825 92.01 0.1889 0.1875 0.188 0.218 0.2188 RANDOM 21.678
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] -0.86 -0.17 0.61 0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.361 r_dihedral_angle_4_deg 17.399 r_dihedral_angle_3_deg 12.348 r_dihedral_angle_1_deg 6.174 r_angle_refined_deg 1.213 r_chiral_restr 0.086 r_gen_planes_refined 0.006 r_bond_refined_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5017 Nucleic Acid Atoms Solvent Atoms 657 Heterogen Atoms 183
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling MOLREP phasing DM phasing REFMAC refinement PDB_EXTRACT data extraction