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Crystal structure of a GNAT superfamily acetyltransferase PA4794 C29A/C117A/Y128A mutant in complex with chloramphenicol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4KUA PDB ENTRY 4KUA
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 2.42 49.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.88 α = 90 b = 75.626 β = 90 c = 39.482 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 2012-11-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.91837 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 1.25 50 99.9 0.053 0.053 43.7 7.3 48658 48658 -3 13.6
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 1.25 1.27 100 0.747 0.747 2.4 6.3 2440
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 PDB ENTRY 4KUA 1.25 45.96 46151 46151 2456 99.92 0.1221 0.1221 0.12037 0.1206 0.15476 0.1526 RANDOM 19.185
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] -0.42 -0.85 1.26
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 42.413 r_dihedral_angle_2_deg 34.3 r_dihedral_angle_4_deg 17.615 r_sphericity_bonded 17.322 r_dihedral_angle_3_deg 11.088 r_rigid_bond_restr 8.645 r_dihedral_angle_1_deg 5.667 r_long_range_B_other 5.334 r_long_range_B_refined 5.331 r_scangle_other 4.818
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 42.413 r_dihedral_angle_2_deg 34.3 r_dihedral_angle_4_deg 17.615 r_sphericity_bonded 17.322 r_dihedral_angle_3_deg 11.088 r_rigid_bond_restr 8.645 r_dihedral_angle_1_deg 5.667 r_long_range_B_other 5.334 r_long_range_B_refined 5.331 r_scangle_other 4.818 r_scbond_other 4.599 r_scbond_it 4.596 r_angle_other_deg 3.504 r_mcangle_other 1.978 r_mcangle_it 1.97 r_angle_refined_deg 1.92 r_mcbond_it 1.773 r_mcbond_other 1.661 r_chiral_restr 0.108 r_bond_refined_d 0.018 r_gen_planes_other 0.015 r_gen_planes_refined 0.01 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_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1239 Nucleic Acid Atoms Solvent Atoms 242 Heterogen Atoms 102
Software Software Software Name Purpose HKL-3000 data collection DENZO data reduction SCALEPACK data scaling REFMAC refinement Coot model building HKL-3000 data reduction HKL-3000 data scaling