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Crystal structure of spermidine/spermine N-acetyltransferase SpeG from Yersinia pestis in complex with calcium ions.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5WIF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 0.1 M Imidazole, 14% (w/v) PEG10000
Crystal Properties Matthews coefficient Solvent content 2.93 58.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.761 α = 90 b = 120.804 β = 90 c = 123.33 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 RAYONIX MX300-HS 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 2.17 30 99.1 0.063 23.3 5.1 40132
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 2.17 2.21 100 0.8 2.03 5.2
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 5WIF 2.17 30 38176 1952 98.98 0.1835 0.18207 0.1883 0.21235 0.2145 RANDOM 55.287
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] 0.61 -2.85 2.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.977 r_dihedral_angle_4_deg 19.419 r_dihedral_angle_3_deg 15.948 r_long_range_B_refined 6.279 r_long_range_B_other 6.262 r_dihedral_angle_1_deg 6.095 r_scangle_other 4.383 r_mcangle_it 3.537 r_mcangle_other 3.537 r_scbond_it 3.279
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.977 r_dihedral_angle_4_deg 19.419 r_dihedral_angle_3_deg 15.948 r_long_range_B_refined 6.279 r_long_range_B_other 6.262 r_dihedral_angle_1_deg 6.095 r_scangle_other 4.383 r_mcangle_it 3.537 r_mcangle_other 3.537 r_scbond_it 3.279 r_scbond_other 3.278 r_mcbond_it 2.439 r_mcbond_other 2.375 r_angle_refined_deg 1.642 r_angle_other_deg 1.004 r_chiral_restr 0.107 r_bond_refined_d 0.015 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 4354 Nucleic Acid Atoms Solvent Atoms 187 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing BLU-MAX data collection