Navigation Tabs Joint X-ray/neutron structure of Thermus thermophilus serine hydroxymethyltransferase (TthSHMT) in internal aldimine state with L-Ser bound in a pre-Michalis complex
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DKJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 289 40 mM NaOAc pH 5.5, 1.0 M (NH4)2SO4, and 0.5 M Li2SO4
Crystal Properties Matthews coefficient Solvent content 2.62 53.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.807 α = 90 b = 83.334 β = 91.68 c = 95.568 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 neutron 293 AREA DETECTOR ORNL ANGER CAMERA 2022-08-10 L LAUE 2 1 x-ray 293 PIXEL DECTRIS EIGER R 4M Osmic Varimax 2022-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SPALLATION SOURCE ORNL Spallation Neutron Source BEAMLINE MANDI 2-4.16 ORNL Spallation Neutron Source MANDI 2 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54
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 2.3 14.43 97 0.228 0.097 0.918 10.3 5.3 39816 2 2 95.59 99.9 0.107 0.059 0.991 13.1 4.4 62552
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 2.3 2.38 95.9 0.245 0.115 0.638 4.7 4.4 2 2 2.07 99.4 0.459 0.258 0.667 2.7 4.2
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 R-Free R-Free Selection Details Mean Isotropic B NEUTRON DIFFRACTION MOLECULAR REPLACEMENT 2.3 40 2.5 39712 1981 97 0.204 0.221 random 17.68 X-RAY DIFFRACTION MOLECULAR REPLACEMENT 2 40 2.5 56331 2853 93.7 0.166 0.183 random 17.68
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 17.3 x_torsion_deg 17.3 x_angle_deg 1 x_angle_deg 1 x_torsion_impr_deg 0.76 x_torsion_impr_deg 0.76 x_bond_d 0.007 x_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6250 Nucleic Acid Atoms Solvent Atoms 396 Heterogen Atoms 17
Software Software Software Name Purpose nCNS refinement CrysalisPro data reduction CrysalisPro data scaling PHASER phasing Mantid data reduction SCALA data scaling
