☰ Navigation Tabs
Spermidine N-acetyltransferase from Vibrio cholerae in complex with 2-[n-cyclohexylamino]ethane sulfonate.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EG7 PDB ENTRY 3EG7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9.5 289 0.2 M lithium sulfate, 0.1 M CHES buffer, 1 M potassium/sodium tartrate, 0.02 M acetylcholine, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.61 52.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.751 α = 90 b = 134.498 β = 90 c = 137.086 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 SBC-3 2008-10-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.9792 APS 19-BM
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 1.89 32.02 98.3 0.067 13.6 7.6 52181 52181
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 1.89 1.93 94.7 0.599 2.76 6.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 3EG7 1.89 32.02 52127 49481 2646 97.56 0.19304 0.19072 0.1966 0.23762 0.2379 RANDOM 43.139
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] 5.14 -4.51 -0.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.451 r_dihedral_angle_4_deg 19.678 r_dihedral_angle_3_deg 15.217 r_dihedral_angle_1_deg 5.862 r_angle_refined_deg 1.769 r_angle_other_deg 0.849 r_chiral_restr 0.105 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.451 r_dihedral_angle_4_deg 19.678 r_dihedral_angle_3_deg 15.217 r_dihedral_angle_1_deg 5.862 r_angle_refined_deg 1.769 r_angle_other_deg 0.849 r_chiral_restr 0.105 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined 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 4308 Nucleic Acid Atoms Solvent Atoms 276 Heterogen Atoms 64
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction SBC-Collect data collection HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing HKL-3000 phasing