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Crystal structure of Medicago truncatula Thermospermine Synthase (MtTSPS)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1INL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 292 10% PEG3350, 0.1 M Magnesium Chloride and 0.1 M MES buffer; cryo 33% PEG400
Crystal Properties Matthews coefficient Solvent content 1.79 31.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.53 α = 90 b = 80.53 β = 90 c = 164.36 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 2017-03-18 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 1.68 46.81 99.7 0.059 20.9 9.4 62270 -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 1.68 1.78 98.4 1.058 2 9.1
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 1INL 1.68 46.81 61210 1059 99.72 0.17626 0.17557 0.185 0.21671 0.2312 RANDOM 31.349
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] -0.17 -0.17 0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.859 r_dihedral_angle_4_deg 25.269 r_dihedral_angle_3_deg 14.588 r_dihedral_angle_1_deg 6.712 r_long_range_B_refined 5.378 r_long_range_B_other 5.378 r_scangle_other 2.945 r_mcangle_it 2.134 r_mcangle_other 2.134 r_scbond_it 1.778
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.859 r_dihedral_angle_4_deg 25.269 r_dihedral_angle_3_deg 14.588 r_dihedral_angle_1_deg 6.712 r_long_range_B_refined 5.378 r_long_range_B_other 5.378 r_scangle_other 2.945 r_mcangle_it 2.134 r_mcangle_other 2.134 r_scbond_it 1.778 r_scbond_other 1.777 r_angle_refined_deg 1.634 r_mcbond_it 1.293 r_mcbond_other 1.292 r_angle_other_deg 1.284 r_chiral_restr 0.104 r_bond_refined_d 0.013 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 4651 Nucleic Acid Atoms Solvent Atoms 302 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing