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Crystal structure of Medicago truncatula serine hydroxymethyltransferase 3 (MtSHMT3) soaked with selenourea
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 292 55% Tacsimate pH 7.0; for SAD phasing crystals were transferred into a drop of 100% Tacsimate pH 7.0 with a single crystal of selenourea and soaked for 15 min
Crystal Properties Matthews coefficient Solvent content 2.48 50.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.675 α = 90 b = 199.686 β = 90 c = 152.498 γ = 90
Symmetry Space Group C 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 100 CCD RAYONIX MX300-HS 2017-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 0.9778 APS 22-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 2.14 100 96.9 0.078 0.085 19.7 6 52956
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 2.14 2.27 81.1 0.55 0.88 3.7 3.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 2.14 83.53 51949 1007 95.7 0.166 0.165 0.1749 0.206 0.2119 RANDOM 35.656
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] -0.46 -1.23 1.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.314 r_dihedral_angle_4_deg 17.724 r_dihedral_angle_3_deg 14.213 r_dihedral_angle_1_deg 6.755 r_long_range_B_refined 5.638 r_long_range_B_other 5.638 r_scangle_other 3.034 r_mcangle_it 2.455 r_mcangle_other 2.455 r_scbond_it 1.826
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.314 r_dihedral_angle_4_deg 17.724 r_dihedral_angle_3_deg 14.213 r_dihedral_angle_1_deg 6.755 r_long_range_B_refined 5.638 r_long_range_B_other 5.638 r_scangle_other 3.034 r_mcangle_it 2.455 r_mcangle_other 2.455 r_scbond_it 1.826 r_scbond_other 1.824 r_angle_refined_deg 1.586 r_mcbond_it 1.453 r_mcbond_other 1.453 r_angle_other_deg 1.007 r_chiral_restr 0.09 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 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 6807 Nucleic Acid Atoms Solvent Atoms 325 Heterogen Atoms 94
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling HKL2Map phasing