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Crystal structure of E33Q and E41Q mutant forms of the spermidine/spermine N-acetyltransferase SpeG from Vibrio cholerae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5CNP PDB ENTRY 5CNP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 0.01 M magnesium chloride, 0.1 M Tris, 10% isopropanol
Crystal Properties Matthews coefficient Solvent content 3.06 59.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 160.235 α = 90 b = 133.016 β = 113.39 c = 77.711 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 2017-04-11 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 2.26 30 98.7 0.06 30.2 3.7 68104
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 2.26 2.3 100 0.64 3.7
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 5CNP 2.26 30 64711 3393 98.2 0.19 0.189 0.1889 0.216 0.2136 RANDOM 74.08
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] -0.45 1.46 -3.02 1.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.601 r_dihedral_angle_4_deg 17.947 r_dihedral_angle_3_deg 15.941 r_long_range_B_refined 7.157 r_dihedral_angle_1_deg 6.634 r_mcangle_it 4.009 r_scbond_it 3.437 r_mcbond_it 2.68 r_angle_refined_deg 1.581 r_chiral_restr 0.112
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.601 r_dihedral_angle_4_deg 17.947 r_dihedral_angle_3_deg 15.941 r_long_range_B_refined 7.157 r_dihedral_angle_1_deg 6.634 r_mcangle_it 4.009 r_scbond_it 3.437 r_mcbond_it 2.68 r_angle_refined_deg 1.581 r_chiral_restr 0.112 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_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 8569 Nucleic Acid Atoms Solvent Atoms 217 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement BLU-MAX data collection HKL-3000 data reduction HKL-3000 data scaling PHASER phasing