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Crystal structure of Medicago truncatula Thermospermine Synthase (MtTSPS) in complex with 5'-S-(3-aminopropyl)-5'-thioadenosine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6BQ2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 292 10% PEG3350, 0.1 M Magnesium Chloride, 0.1 M MES buffer; cryo 33% PEG400, 10% PEG3350, 0.1 M Magnesium Chloride, Bis-Tris propane pH 6.5
Crystal Properties Matthews coefficient Solvent content 1.8 31.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.052 α = 90 b = 81.052 β = 90 c = 163.128 γ = 90
Symmetry Space Group P 43 21 2
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 2017-08-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 72.59 99.9 0.075 17.4 5.6 43034 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.91 2 100 0.741 2.1 5.6
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6BQ2 1.91 72.59 41900 1060 99.84 0.19034 0.18913 0.1958 0.23793 0.2351 RANDOM 41.683
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] -0.09 -0.09 0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.656 r_dihedral_angle_4_deg 26.114 r_dihedral_angle_3_deg 15.156 r_dihedral_angle_1_deg 6.954 r_long_range_B_refined 4.192 r_long_range_B_other 4.192 r_scangle_other 2.216 r_mcangle_it 1.861 r_mcangle_other 1.861 r_angle_refined_deg 1.614
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.656 r_dihedral_angle_4_deg 26.114 r_dihedral_angle_3_deg 15.156 r_dihedral_angle_1_deg 6.954 r_long_range_B_refined 4.192 r_long_range_B_other 4.192 r_scangle_other 2.216 r_mcangle_it 1.861 r_mcangle_other 1.861 r_angle_refined_deg 1.614 r_scbond_it 1.399 r_scbond_other 1.399 r_mcbond_it 1.217 r_mcbond_other 1.217 r_angle_other_deg 0.988 r_chiral_restr 0.1 r_bond_refined_d 0.014 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 4672 Nucleic Acid Atoms Solvent Atoms 163 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing