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Crystal structure of Medicago truncatula Thermospermine Synthase (MtTSPS) in complex with thermospermine
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 Bis-Tris propane buffer
cryo 33% PEG400
Crystal Properties Matthews coefficient Solvent content 1.76 30.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.293 α = 90 b = 80.293 β = 90 c = 163.245 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 PIXEL DECTRIS PILATUS 6M 2017-04-06 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) 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 1.65 46.61 99.8 0.068 23.5 12.8 65012 -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 1.65 1.75 99.1 1.287 2.1 12.8
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 6BQ2 1.65 46.61 63970 1041 99.84 0.17303 0.17211 0.23027 0.2088 RANDOM 29.913
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] -0.12 -0.12 0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.598 r_dihedral_angle_4_deg 26.82 r_dihedral_angle_3_deg 14.674 r_dihedral_angle_1_deg 6.932 r_long_range_B_refined 5.524 r_long_range_B_other 5.523 r_scangle_other 3.102 r_mcangle_it 2.403 r_mcangle_other 2.403 r_scbond_it 1.888
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.598 r_dihedral_angle_4_deg 26.82 r_dihedral_angle_3_deg 14.674 r_dihedral_angle_1_deg 6.932 r_long_range_B_refined 5.524 r_long_range_B_other 5.523 r_scangle_other 3.102 r_mcangle_it 2.403 r_mcangle_other 2.403 r_scbond_it 1.888 r_scbond_other 1.887 r_angle_refined_deg 1.681 r_mcbond_it 1.48 r_mcbond_other 1.479 r_angle_other_deg 0.997 r_chiral_restr 0.105 r_bond_refined_d 0.014 r_gen_planes_refined 0.009 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 4663 Nucleic Acid Atoms Solvent Atoms 341 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing