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Crystal structure of spermidine N-acetyltransferase from Vibrio cholerae in complex with CoA and spermine
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 293 0.2 M Sodium citrate, 20% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.41 48.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 176.948 α = 90 b = 176.948 β = 90 c = 67.009 γ = 120
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 2013-11-26 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 2.6 50 96.2 0.17 15.04 4.7 68437 68437 -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 2.6 2.64 100 0.62 2.9 5.3
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 3EG7 2.61 43.82 72802 64716 3380 95.65 0.1875 0.18488 0.2383 0.2318 RANDOM 37.435
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] 12.75 12.75 -25.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.347 r_dihedral_angle_3_deg 18.15 r_dihedral_angle_4_deg 17.724 r_dihedral_angle_1_deg 7.798 r_long_range_B_refined 5.947 r_mcangle_it 2.834 r_angle_refined_deg 1.912 r_scbond_it 1.778 r_mcbond_it 1.774 r_mcbond_other 1.774
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.347 r_dihedral_angle_3_deg 18.15 r_dihedral_angle_4_deg 17.724 r_dihedral_angle_1_deg 7.798 r_long_range_B_refined 5.947 r_mcangle_it 2.834 r_angle_refined_deg 1.912 r_scbond_it 1.778 r_mcbond_it 1.774 r_mcbond_other 1.774 r_angle_other_deg 0.892 r_chiral_restr 0.245 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 17167 Nucleic Acid Atoms Solvent Atoms 347 Heterogen Atoms 631
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling