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Crystal structure of a GNAT superfamily acetyltransferase PA4794 in complex with 2-(aminocarbonyl)benzoate
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 2.35 47.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.962 α = 90 b = 75.957 β = 90 c = 39.16 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 MARMOSAIC 225 mm CCD Beryllium Lenses 2010-07-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.9787 APS 21-ID-F
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 1.3 50 99.5 0.06 0.06 38.5 5.5 42231 42231 -3 13.4
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 1.3 1.32 94.1 0.423 0.423 2 2.9 1965
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 1.3 32.29 40053 40053 2133 99.31 0.14071 0.14071 0.13891 0.1397 0.17439 0.175 RANDOM 20.051
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] 0.03 0.18 -0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.712 r_dihedral_angle_4_deg 17.42 r_dihedral_angle_3_deg 14.276 r_sphericity_bonded 12.314 r_rigid_bond_restr 6.951 r_dihedral_angle_1_deg 5.53 r_angle_other_deg 3.62 r_angle_refined_deg 1.853 r_chiral_restr 0.126 r_gen_planes_other 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.712 r_dihedral_angle_4_deg 17.42 r_dihedral_angle_3_deg 14.276 r_sphericity_bonded 12.314 r_rigid_bond_restr 6.951 r_dihedral_angle_1_deg 5.53 r_angle_other_deg 3.62 r_angle_refined_deg 1.853 r_chiral_restr 0.126 r_gen_planes_other 0.02 r_bond_refined_d 0.019 r_gen_planes_refined 0.011 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_scbond_it r_scangle_it r_sphericity_free
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1241 Nucleic Acid Atoms Solvent Atoms 308 Heterogen Atoms 44
Software Software Software Name Purpose LS-CAT modified MD-2 data collection HKL-3000 phasing REFMAC refinement Coot model building HKL-3000 data reduction HKL-3000 data scaling