☰ Navigation Tabs
Crystal structure of Medicago truncatula serine hydroxymethyltransferase 3 (MtSHMT3), complexes with reaction intermediates
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6CCZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 292 75 mM MES pH 6.5, 19% PEG3350 and 150 mM ammonium acetate. The mature crystals were soaked with 200 mM Ser for 2 h and cryoprotected by the addition of ethylene glycol to a final concentration of 20%
Crystal Properties Matthews coefficient Solvent content 2.19 43.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.086 α = 90 b = 103.653 β = 97.38 c = 180.379 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 x-ray 100 PIXEL DECTRIS PILATUS 6M 2017-11-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9792 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (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 1.91 50 98.6 0.063 0.071 13.3 4.7 263165
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.91 2.02 97.3 0.73 0.83 1.9 4.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6ccz 1.91 46.65 261832 1316 98.6 0.191 0.191 0.236 0.2332 RANDOM 40.906
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] -0.77 0.43 1.24 -0.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.369 r_dihedral_angle_3_deg 14.302 r_dihedral_angle_4_deg 13.195 r_dihedral_angle_1_deg 6.432 r_long_range_B_refined 5.185 r_long_range_B_other 5.185 r_scangle_other 2.227 r_mcangle_it 1.886 r_mcangle_other 1.886 r_angle_refined_deg 1.529
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.369 r_dihedral_angle_3_deg 14.302 r_dihedral_angle_4_deg 13.195 r_dihedral_angle_1_deg 6.432 r_long_range_B_refined 5.185 r_long_range_B_other 5.185 r_scangle_other 2.227 r_mcangle_it 1.886 r_mcangle_other 1.886 r_angle_refined_deg 1.529 r_scbond_it 1.322 r_scbond_other 1.322 r_mcbond_it 1.163 r_mcbond_other 1.163 r_angle_other_deg 0.98 r_chiral_restr 0.087 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 27693 Nucleic Acid Atoms Solvent Atoms 2032 Heterogen Atoms 138
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing