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Crystal structure of spermidine/spermine N-acetyltransferase SpeG from Vibrio cholerae in complex with manganese ions.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4NCZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 0.2 M Trimethylamine N-oxide, 0.1 M Tris, 20% w/v PEG2000 MME
Crystal Properties Matthews coefficient Solvent content 2.74 55.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 157.645 α = 90 b = 135.267 β = 118.58 c = 73.675 γ = 90
Symmetry Space Group C 1 2 1
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 RAYONIX MX-300 Beryllium Lenses 2016-03-21 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 2.4 30 94.3 0.063 26.7 3.4 49284
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 2.4 2.44 97.7 0.52 2.4
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 4NCZ 2.41 30 46921 2363 93.68 0.17346 0.17137 0.1775 0.21319 0.2152 RANDOM 56.615
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] -0.97 -1.61 0.13 1.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.586 r_dihedral_angle_4_deg 14.832 r_dihedral_angle_3_deg 12.755 r_long_range_B_other 9.226 r_long_range_B_refined 9.222 r_scangle_other 7.547 r_mcangle_it 5.626 r_mcangle_other 5.626 r_scbond_it 5.592 r_scbond_other 5.591
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.586 r_dihedral_angle_4_deg 14.832 r_dihedral_angle_3_deg 12.755 r_long_range_B_other 9.226 r_long_range_B_refined 9.222 r_scangle_other 7.547 r_mcangle_it 5.626 r_mcangle_other 5.626 r_scbond_it 5.592 r_scbond_other 5.591 r_mcbond_it 4.183 r_mcbond_other 4.18 r_dihedral_angle_1_deg 3.734 r_angle_refined_deg 2.158 r_angle_other_deg 1.073 r_chiral_restr 0.142 r_gen_planes_refined 0.026 r_bond_refined_d 0.02 r_gen_planes_other 0.019 r_bond_other_d 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 8616 Nucleic Acid Atoms Solvent Atoms 206 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement BLU-MAX data collection HKL-3000 data scaling HKL-3000 data reduction PHASER phasing Coot model building