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The external aldimine form of the Salmonella thypi wild-type tryptophan synthase in open conformation showing multiple side chain conformations for the residue beta Q114 and sodium ion at the metal coordination site. One of the beta-Q114 rotamer conformations 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 4HN4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.8 293 50 mM Bicine-NaOH, 10% PEG 8,000, 2 mM Spermine, pH 7.8, 50mM NaCl
Crystal Properties Matthews coefficient Solvent content 2.34 47.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 182.655 α = 90 b = 59.415 β = 94.89 c = 67.345 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 315r 2019-04-18 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 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 1.398 90.995 99.6 0.093 0.102 0.042 9 5.6 141196 141196
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 1.4 1.48 98.4 0.92 0.92 1.014 0.418 0.8 5.3
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 4HN4 1.4 36.91 134277 6919 99.38 0.1634 0.1618 0.1615 0.1949 0.1947 RANDOM 22.033
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] 0.02 0.01 -0.05 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.466 r_dihedral_angle_4_deg 17.707 r_dihedral_angle_3_deg 12.385 r_rigid_bond_restr 7.311 r_dihedral_angle_1_deg 6.242 r_angle_refined_deg 1.526 r_chiral_restr 0.101 r_gen_planes_refined 0.009 r_bond_refined_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4906 Nucleic Acid Atoms Solvent Atoms 790 Heterogen Atoms 126
Software Software Software Name Purpose SCALA data scaling PHASER phasing DM phasing REFMAC refinement PDB_EXTRACT data extraction