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Crystal structure of a GNAT superfamily acetyltransferase PA4794 in ternary complex with N-Phenylacetyl-Gly-AcLys and CoA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2I6C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 289 2M ammonium sulfate, 0.1M Bis Tris pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.4 48.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.207 α = 90 b = 76.669 β = 90 c = 39.4 γ = 90
Symmetry Space Group P 21 21 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 ADSC QUANTUM 315r mirrors 2011-10-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97912 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.2 50 100 0.046 0.046 62.2 8.7 55044 55044 -3 14.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.2 1.22 100 0.564 0.564 2.8 6.1 2703
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 (All) 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 2i6c 1.2 45.85 52186 52186 2787 99.97 0.1303 0.1303 0.12893 0.1306 0.15599 0.1583 RANDOM 18.928
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 -0.17 -0.28
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 37.124 r_dihedral_angle_2_deg 36.921 r_sphericity_bonded 14.058 r_dihedral_angle_4_deg 13.388 r_dihedral_angle_3_deg 11.414 r_rigid_bond_restr 7.878 r_dihedral_angle_1_deg 5.729 r_angle_other_deg 3.554 r_angle_refined_deg 1.972 r_chiral_restr 0.11
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 37.124 r_dihedral_angle_2_deg 36.921 r_sphericity_bonded 14.058 r_dihedral_angle_4_deg 13.388 r_dihedral_angle_3_deg 11.414 r_rigid_bond_restr 7.878 r_dihedral_angle_1_deg 5.729 r_angle_other_deg 3.554 r_angle_refined_deg 1.972 r_chiral_restr 0.11 r_gen_planes_other 0.017 r_bond_refined_d 0.016 r_gen_planes_refined 0.012 r_bond_other_d 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1236 Nucleic Acid Atoms Solvent Atoms 280 Heterogen Atoms 123
Software Software Software Name Purpose HKL-3000 data collection HKL-3000 phasing REFMAC refinement Coot model building HKL-3000 data reduction HKL-3000 data scaling