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Crystal structure of spermidine/spermine N-acetyltransferase SpeG from Escherichia coli in complex with tris(hydroxymethyl)aminomethane.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4R9M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 0.2 M Ammonium phosphate monobasic, 0.1 M Tris, 50% v/v MPD
Crystal Properties Matthews coefficient Solvent content 2.47 50.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.499 α = 90 b = 107.499 β = 90 c = 65.021 γ = 120
Symmetry Space Group P 6 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 2016-11-15 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) CC (Half) 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 1.75 30 100 0.048 0.048 51.1 12.8 22903
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 1.75 1.78 100 0.65 4.3 13
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 4R9M 1.75 93.1 21759 1144 99.88 0.15587 0.15352 0.1683 0.20067 0.2054 RANDOM 31.44
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] -0.32 -0.16 -0.32 1.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.246 r_dihedral_angle_4_deg 20.06 r_dihedral_angle_3_deg 11.266 r_long_range_B_refined 7.607 r_long_range_B_other 7.526 r_scangle_other 6.204 r_scbond_it 4.317 r_scbond_other 4.28 r_dihedral_angle_1_deg 4.025 r_mcangle_it 3.148
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.246 r_dihedral_angle_4_deg 20.06 r_dihedral_angle_3_deg 11.266 r_long_range_B_refined 7.607 r_long_range_B_other 7.526 r_scangle_other 6.204 r_scbond_it 4.317 r_scbond_other 4.28 r_dihedral_angle_1_deg 4.025 r_mcangle_it 3.148 r_mcangle_other 3.146 r_mcbond_it 2.237 r_mcbond_other 2.225 r_angle_refined_deg 2.098 r_angle_other_deg 1.005 r_chiral_restr 0.132 r_gen_planes_refined 0.025 r_bond_refined_d 0.021 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 1422 Nucleic Acid Atoms Solvent Atoms 105 Heterogen Atoms 65
Software Software Software Name Purpose REFMAC refinement BLU-MAX data collection HKL-3000 data scaling HKL-3000 data reduction Coot model building PHASER phasing