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Salmonella typhimurium Tryptophan Synthase beta-S377A mutant in complex with inhibitor F9 at the enzyme alpha-site, cesium ion at the metal coordination site and carbanion III E(C3) at the enzyme beta-site.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4HPJ
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 2.53 51.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 181.517 α = 90 b = 59.427 β = 94.64 c = 67.063 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 2019-04-19 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 1.55 90.461 95 0.05 0.078 0.039 10.8 3.8 97942 97942
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 1.55 1.63 73 0.163 0.163 0.26 0.154 4.1 2.7
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 4HPJ 1.55 38.95 92932 4983 94.69 0.1771 0.1739 0.1737 0.2357 0.2358 RANDOM 22.523
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] 0.03 0.1 0.28 -0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.715 r_dihedral_angle_4_deg 17.556 r_dihedral_angle_3_deg 13.192 r_dihedral_angle_1_deg 6.341 r_rigid_bond_restr 2.134 r_angle_refined_deg 1.369 r_chiral_restr 0.092 r_gen_planes_refined 0.007 r_bond_refined_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5017 Nucleic Acid Atoms Solvent Atoms 770 Heterogen Atoms 159
Software Software Software Name Purpose xia2 data reduction SCALA data scaling MOLREP phasing DM phasing REFMAC refinement PDB_EXTRACT data extraction