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Joint X-ray/neutron structure of E53Q mutant of Thermus thermophilus serine hydroxymethyltransferase (TthSHMT)
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8SUJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 289 40 mM NaOAc, pH 5.5, 1M ammonium sulfate, 0.5 M lithium sulfate
Crystal Properties Matthews coefficient Solvent content 2.62 53.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.819 α = 90 b = 83.522 β = 91.64 c = 95.425 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 2024-10-02 L LAUE 2 1 x-ray 293 PIXEL DECTRIS EIGER R 4M 2024-10-03 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 1.5406
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 2.4 58.8 77.3 0.183 0.101 0.957 3.8 3.5 28304 2 1.65 95.4 99.1 0.067 0.039 0.967 19.1 3.8 109873
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 2.4 2.52 0.301 0.171 0.686 2.3 3.1 2 1.65 1.71 0.361 0.251 0.823 2.5 2.4
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 2.4 40 2.5 23605 1120 65.1 0.236 0.263 random 19.89 X-RAY DIFFRACTION MOLECULAR REPLACEMENT 1.65 29.4 2.5 98994 5014 89.3 0.189 0.3423 0.197 0.3421 random 19.89
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 19 x_torsion_deg 19 x_torsion_impr_deg 1.12 x_torsion_impr_deg 1.12 x_angle_deg 1.1 x_angle_deg 1.1 x_bond_d 0.009 x_bond_d 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6250 Nucleic Acid Atoms Solvent Atoms 505 Heterogen Atoms 10
Software Software Software Name Purpose LAUEGEN data reduction CrysalisPro data reduction LSCALE data scaling SCALA data scaling Aimless data scaling PHASER phasing nCNS refinement