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Crystal structure of a GNAT superfamily acetyltransferase PA4794 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 2.41 48.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.754 α = 90 b = 76.072 β = 90 c = 39.483 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 2013-06-23 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 1.45 50 99.7 0.043 0.043 46.9 5.4 31335 31335 -3 21.8
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 1.45 1.48 100 0.716 0.716 2.3 5.4 1539
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 1.45 46 29702 29702 1583 99.01 0.15496 0.15496 0.1536 0.1537 0.17924 0.1794 RANDOM 23.483
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] -0.52 -0.35 0.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.343 r_dihedral_angle_4_deg 17.932 r_dihedral_angle_3_deg 12.171 r_long_range_B_refined 7.184 r_long_range_B_other 6.721 r_dihedral_angle_1_deg 5.847 r_scangle_other 3.858 r_angle_other_deg 3.543 r_scbond_it 2.615 r_scbond_other 2.606
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.343 r_dihedral_angle_4_deg 17.932 r_dihedral_angle_3_deg 12.171 r_long_range_B_refined 7.184 r_long_range_B_other 6.721 r_dihedral_angle_1_deg 5.847 r_scangle_other 3.858 r_angle_other_deg 3.543 r_scbond_it 2.615 r_scbond_other 2.606 r_mcangle_it 1.905 r_mcangle_other 1.905 r_angle_refined_deg 1.881 r_mcbond_it 1.282 r_mcbond_other 1.252 r_chiral_restr 0.117 r_bond_refined_d 0.018 r_gen_planes_other 0.017 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1241 Nucleic Acid Atoms Solvent Atoms 217 Heterogen Atoms 92
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