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Structure of spermidine N-acetyltransferase SpeG from Vibrio cholerae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4MI4 PDB entry 4MI4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 294 0.1 M Tris, 50% MPD, 20% ethanol
Crystal Properties Matthews coefficient Solvent content 2.68 54.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.884 α = 90 b = 134.635 β = 90 c = 137.346 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 300 mm CCD beryllium lenses 2011-10-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97857 APS 21-ID-G
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 2.15 30 99.4 0.09 28.5 14.9 36218
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 2.15 2.2 98.2 0.39 8.3 15 1771
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 4MI4 2.15 30 34406 1812 98.64 0.17088 0.16929 0.1768 0.19986 0.2045 RANDOM 39.589
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] -0.19 -1.26 1.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.703 r_dihedral_angle_4_deg 22.328 r_dihedral_angle_3_deg 14.735 r_dihedral_angle_1_deg 6.246 r_long_range_B_refined 5.942 r_long_range_B_other 5.942 r_scangle_other 4.307 r_mcangle_it 2.943 r_mcangle_other 2.942 r_scbond_it 2.773
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.703 r_dihedral_angle_4_deg 22.328 r_dihedral_angle_3_deg 14.735 r_dihedral_angle_1_deg 6.246 r_long_range_B_refined 5.942 r_long_range_B_other 5.942 r_scangle_other 4.307 r_mcangle_it 2.943 r_mcangle_other 2.942 r_scbond_it 2.773 r_scbond_other 2.773 r_mcbond_it 2.013 r_mcbond_other 1.976 r_angle_refined_deg 1.919 r_angle_other_deg 1.079 r_chiral_restr 0.119 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 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 4313 Nucleic Acid Atoms Solvent Atoms 236 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing