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Crystal structure of spermidine N-acetyltransferase from Vibrio cholerae in complex with spermidine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EG7 PDB entry 3EG7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 0.1 M NaCl, 30% Ethanol, 0.1M Tris HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.48 50.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.453 α = 90 b = 136.012 β = 90 c = 139.831 γ = 90
Symmetry Space Group I 2 2 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 MARMOSAIC 225 mm CCD Beryllium lenses 2011-11-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
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 2.3 30 98.8 0.064 43.8 7.2 30239 30239 -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 2.3 2.34 100 0.23 7.9 7.4
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 3EG7 2.32 29.33 28715 28715 1522 97.93 0.19852 0.19561 0.1981 0.25377 0.2488 RANDOM 54.973
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] 0.38 -0.44 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.774 r_dihedral_angle_4_deg 16.546 r_dihedral_angle_3_deg 10.92 r_long_range_B_refined 6.824 r_long_range_B_other 6.816 r_scangle_other 5.254 r_scbond_it 3.802 r_scbond_other 3.801 r_mcangle_it 3.787 r_mcangle_other 3.786
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.774 r_dihedral_angle_4_deg 16.546 r_dihedral_angle_3_deg 10.92 r_long_range_B_refined 6.824 r_long_range_B_other 6.816 r_scangle_other 5.254 r_scbond_it 3.802 r_scbond_other 3.801 r_mcangle_it 3.787 r_mcangle_other 3.786 r_dihedral_angle_1_deg 3.477 r_mcbond_it 2.774 r_mcbond_other 2.773 r_angle_refined_deg 1.921 r_angle_other_deg 0.859 r_chiral_restr 0.129 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 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 4322 Nucleic Acid Atoms Solvent Atoms 128 Heterogen Atoms 30
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling