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293 K Structure of Human Spermidine Synthase in Complex with 5-deoxy-5-methylthioadenosine and Putrescine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2O07
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 294 0.05-0.225 M sodium sulfate, 0.1 M Bis-Tris pH 5.5, 6.5-23% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.1 41.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.974 α = 90 b = 61.376 β = 108.566 c = 86.907 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 293 PIXEL DECTRIS EIGER2 XE 16M 2025-12-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-1 0.97946 SSRL BL12-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.94 82.38 96.9 0.149 0.184 0.106 0.985 3.9 2.8 42266 19.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.94 2.04 99.3 0.891 1.104 0.644 0.457 2.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS FREE R-VALUE 1.94 41.33 1.34 40037 2153 96.29 0.1676 0.1655 0.1657 0.2066 0.2068 24.15
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.1461 f_angle_d 0.7205 f_chiral_restr 0.0538 f_bond_d 0.0087 f_plane_restr 0.0061
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4516 Nucleic Acid Atoms Solvent Atoms 380 Heterogen Atoms 52
Software Software Software Name Purpose PHENIX refinement autoPROC data scaling autoPROC data reduction PDB_EXTRACT data extraction Coot model building autoPROC data reduction