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The external aldimine form of the mutant beta-S377A Salmonella thypi tryptophan synthase in open conformation showing dual side chain conformations for the residue beta-Q114, sodium ion at the metal coordination site, and F9 inhibitor at the alpha-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 6C73
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.6 298 50 mM Bicine-CsOH, 8% PEG 8,000, 6 mM Spermine, pH 7.6
Crystal Properties Matthews coefficient Solvent content 2.48 50.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 181.38 α = 90 b = 58.244 β = 94.33 c = 67.154 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 2019-12-07 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) 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 1.599 90.431 93.2 0.043 0.043 0.065 0.036 12.8 3.1 85831
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 1.6 1.69 79.4 0.132 0.132 0.179 0.101 5.1 2.9
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 6C73 1.6 38.86 81498 4272 92.88 0.1593 0.1581 0.1579 0.1836 0.1833 RANDOM 15.347
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 0.02 -0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.935 r_dihedral_angle_4_deg 18.289 r_dihedral_angle_3_deg 11.782 r_dihedral_angle_1_deg 6.137 r_angle_refined_deg 1.523 r_chiral_restr 0.097 r_gen_planes_refined 0.009 r_bond_refined_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5017 Nucleic Acid Atoms Solvent Atoms 833 Heterogen Atoms 200
Software Software Software Name Purpose xia2 data reduction SCALA data scaling MOLREP phasing DM phasing REFMAC refinement PDB_EXTRACT data extraction