☰ Navigation Tabs
Room-temperature X-ray structure of human mitochondrial serine hydroxymethyltransferase (hSHMT2) with PLP-glycine external aldimine and 5-formyltetrahydrofolate (folinic acid)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8SSJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.6 293.15 0.5 M Gly pH 8.6, 10 mM folinic acid, 18% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.8 56.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 142.98 α = 90 b = 119.3 β = 90 c = 134.627 γ = 90
Symmetry Space Group P 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293 PIXEL DECTRIS PILATUS 6M 2023-02-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.979 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.1 50 93.4 0.113 0.062 0.987 12.9 4.4 125654
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.14 0.739 0.427 0.483 2.2 4.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.1 42.82 1 122017 6066 90.64 0.1636 0.1623 0.157 0.1886 0.1786
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 f_dihedral_angle_d 16.272 f_angle_d 0.973 f_chiral_restr 0.051 f_plane_restr 0.014 f_bond_d 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14292 Nucleic Acid Atoms Solvent Atoms 765 Heterogen Atoms 216
Software Software Software Name Purpose PHENIX refinement HKL-3000 data scaling HKL-3000 data reduction PHASER phasing