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Crystal structure of Salmonella typhimurium Tryptophan Synthase with sodium ion at the metal coordination site and (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-serine at the beta-site
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 7.8 297 50mM Bicine-NaOH, pH 7.8, containing 9% PEG3350, 50mM NaCl, 2mM spermine
Crystal Properties Matthews coefficient Solvent content 2.54 51.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 182.509 α = 90 b = 59.3 β = 94.69 c = 67.325 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 315 2015-04-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 12.3.1 0.97930 ALS 12.3.1
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 1.45 30 99.5 0.085 0.085 0.094 0.039 0.998 9.9 5.6 126505 126505
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) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.45 1.53 98.1 0.632 0.041 0.045 0.018 0.859 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 1.45 28.94 120118 6241 99.46 0.1488 0.1469 0.1487 0.1856 0.1868 RANDOM 23.82
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] -0.41 0.05 0.11 0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.401 r_sphericity_free 27.023 r_dihedral_angle_4_deg 18.262 r_sphericity_bonded 13.018 r_dihedral_angle_3_deg 11.997 r_dihedral_angle_1_deg 6.052 r_rigid_bond_restr 1.788 r_angle_refined_deg 1.376 r_chiral_restr 0.091 r_gen_planes_refined 0.008
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.401 r_sphericity_free 27.023 r_dihedral_angle_4_deg 18.262 r_sphericity_bonded 13.018 r_dihedral_angle_3_deg 11.997 r_dihedral_angle_1_deg 6.052 r_rigid_bond_restr 1.788 r_angle_refined_deg 1.376 r_chiral_restr 0.091 r_gen_planes_refined 0.008 r_bond_refined_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4922 Nucleic Acid Atoms Solvent Atoms 767 Heterogen Atoms 80
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing