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Crystal Structure of Arabidopsis thaliana Spermidine Synthase isoform 2 (AtSPDS2)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 292 Morpheus screen G4 (Carboxylic acids, buffer system 1, precipitant mix 4)
Crystal Properties Matthews coefficient Solvent content 2.37 48.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.646 α = 90 b = 162.699 β = 100.21 c = 97.494 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 CCD RAYONIX MX300-HS 2018-11-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1.00 APS 22-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 46 97.1 0.056 0.999 16.5 4.3 125268 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.07 97.1 0.557 0.844 2.5 4.3
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 MOLECULAR REPLACEMENT THROUGHOUT 2 42.54 124006 1234 80.16 0.17659 0.17605 0.1849 0.23052 0.23 RANDOM 35.204
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] -0.04 0.41 -0.36 0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.453 r_dihedral_angle_3_deg 16.032 r_dihedral_angle_4_deg 14.39 r_dihedral_angle_1_deg 8.394 r_long_range_B_refined 5.593 r_long_range_B_other 5.552 r_scangle_other 3.244 r_mcangle_it 2.95 r_mcangle_other 2.95 r_scbond_other 1.996
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.453 r_dihedral_angle_3_deg 16.032 r_dihedral_angle_4_deg 14.39 r_dihedral_angle_1_deg 8.394 r_long_range_B_refined 5.593 r_long_range_B_other 5.552 r_scangle_other 3.244 r_mcangle_it 2.95 r_mcangle_other 2.95 r_scbond_other 1.996 r_scbond_it 1.995 r_angle_refined_deg 1.855 r_mcbond_it 1.798 r_mcbond_other 1.798 r_angle_other_deg 1.373 r_chiral_restr 0.092 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 17482 Nucleic Acid Atoms Solvent Atoms 936 Heterogen Atoms 131
Software Software Software Name Purpose REFMAC refinement XDS data reduction STARANISO data scaling PHASER phasing