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Crystal Structure of Spermidine Synthase in Complex with Transition State Analogue AdoDATO
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1INL PDB ENTRY 1INL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 300 PEG 4000, sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal Properties Matthews coefficient Solvent content 2.48 50.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 132.519 α = 90 b = 198.02 β = 90 c = 51.731 γ = 90
Symmetry Space Group P 21 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 SBC-1 2001-05-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97948 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 1.75 50 91.3 0.076 3 138175 126154 15.1
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) 1.75 1.81 72.5 0.566 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 PDB ENTRY 1INL 1.8 46.38 127142 118242 5940 93 0.196 0.196 0.1973 0.229 0.1979 RANDOM 22.2
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] -2.47 -1.72 4.19
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.6 c_scangle_it 4.8 c_scbond_it 3.49 c_mcangle_it 2.83 c_mcbond_it 2.25 c_angle_deg 1.4 c_improper_angle_d 1.26 c_bond_d 0.009 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.6 c_scangle_it 4.8 c_scbond_it 3.49 c_mcangle_it 2.83 c_mcbond_it 2.25 c_angle_deg 1.4 c_improper_angle_d 1.26 c_bond_d 0.009 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9484 Nucleic Acid Atoms Solvent Atoms 743 Heterogen Atoms 87
Software Software Software Name Purpose CNS refinement d*TREK data reduction SCALEPACK data scaling CNS phasing