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Joint X-ray/neutron structure of Salmonella typhimurium tryptophan synthase internal aldimine from microgravity-grown crystal
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BKS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIQUID DIFFUSION 7.8 295 50 mM Bicine pH 7.8, 1 mM EDTA, 0.2 mM PLP, 2 mM spermine, and 6-8% PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.68 54.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 184.51 α = 90 b = 61.86 β = 94.74 c = 67.67 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 289 PIXEL DECTRIS EIGER R 4M 2020-01-27 M SINGLE WAVELENGTH 2 1 neutron 289 IMAGE PLATE LADI III 2021-07-10 L LAUE
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54 2 NUCLEAR REACTOR ILL BEAMLINE LADI III 2.85-3.8 ILL LADI III
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) R Split (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 1.8 91.91 93 0.052 26.6 3 65668 2 2.1 52.36 70.1 0.182 10.4 6.8 30993
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) R Split (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.86 0.311 2.4 2 2 2.1 2.21 0.41 2 5.7
Refinement Statistics Diffraction ID Structure Solution Method Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1.8 29.44 70615 62584 3124 88.6 0.182 0.199 RANDOM 46.29 NEUTRON DIFFRACTION MOLECULAR REPLACEMENT 2.1 37.6 44653 26890 1341 60.2 0.224 0.288 RANDOM 46.29
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]
RMS Deviations Key Refinement Restraint Deviation x_torsion_deg 28.2 x_torsion_deg 28.2 x_angle_deg 1.1 x_angle_deg 1.1 x_torsion_impr_deg 0.8 x_torsion_impr_deg 0.8 x_bond_d 0.009 x_bond_d 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4939 Nucleic Acid Atoms Solvent Atoms 256 Heterogen Atoms 1
Software Software Software Name Purpose nCNS refinement CrysalisPro data reduction CrysalisPro data scaling LAUEGEN data reduction LSCALE data scaling