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Crystal structure of spermidine N-acetyltransferase from Vibrio cholerae in complex with acetyl-CoA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EG7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2 M Sodium Chloride, 20 % PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.4 48.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 176.732 α = 90 b = 176.732 β = 90 c = 67.045 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 2013-11-06 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 2.079 40.6 99.4 0.084 38.1 5.4 140107 140107 -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 2.079 2.12 95.2 0.58 2.8 5
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 3EG7 2.079 40.6 132888 132888 7188 99.42 0.17417 0.17064 0.2195 0.23957 0.2842 RANDOM 36.75
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] 2.39 2.39 -4.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.185 r_dihedral_angle_4_deg 17.987 r_dihedral_angle_3_deg 17.492 r_dihedral_angle_1_deg 7.42 r_long_range_B_refined 5.376 r_long_range_B_other 5.376 r_scangle_other 3.238 r_mcangle_it 3.025 r_mcangle_other 3.025 r_scbond_it 2.178
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.185 r_dihedral_angle_4_deg 17.987 r_dihedral_angle_3_deg 17.492 r_dihedral_angle_1_deg 7.42 r_long_range_B_refined 5.376 r_long_range_B_other 5.376 r_scangle_other 3.238 r_mcangle_it 3.025 r_mcangle_other 3.025 r_scbond_it 2.178 r_scbond_other 2.178 r_mcbond_it 2.109 r_mcbond_other 2.092 r_angle_refined_deg 1.755 r_angle_other_deg 0.884 r_chiral_restr 0.101 r_bond_refined_d 0.013 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 17191 Nucleic Acid Atoms Solvent Atoms 278 Heterogen Atoms 643
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling