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Joint X-ray/neutron structure of Thermus thermophilus serine hydroxymethyltransferase (TthSHMT) in internal aldimine state
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 IMAGE PLATE MAATEL IMAGINE elliptical mirrors 2022-03-29 L LAUE 2 1 x-ray 293 PIXEL DECTRIS EIGER R 4M Osmic VariMax 2022-05-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 NUCLEAR REACTOR ORNL High Flux Isotope Reactor BEAMLINE CG4D 2.8-4.5 ORNL High Flux Isotope Reactor CG4D 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 47.78 85.4 0.161 0.08 0.943 4.3 4.1 32586 2 2 95.54 99.9 0.091 0.044 0.993 17.3 5.4 62364
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 2.42 0.281 0.145 0.637 2.9 3.8 2 2 2.07 0.364 0.1177 0.882 3.9 5.2
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 (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B NEUTRON DIFFRACTION MOLECULAR REPLACEMENT 2.3 40 2.5 31065 1553 75.5 0.21 0.239 random 18.35 X-RAY DIFFRACTION MOLECULAR REPLACEMENT 2 40 2.5 58902 2954 94.4 0.164 0.3363 0.177 0.3361 random 18.35
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 18 x_torsion_deg 18 x_angle_deg 1 x_angle_deg 1 x_torsion_impr_deg 0.79 x_torsion_impr_deg 0.79 x_bond_d 0.008 x_bond_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6250 Nucleic Acid Atoms Solvent Atoms 429 Heterogen Atoms 10
Software Software Software Name Purpose nCNS refinement CrysalisPro data reduction CrysalisPro data scaling PHASER phasing SCALA data scaling LAUEGEN data reduction