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Crystal structure of a GNAT superfamily acetyltransferase PA4794 in complex with 7-aminocephalosporanic acid
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 47.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.827 α = 90 b = 75.992 β = 90 c = 39.103 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 1.25 50 99.2 0.059 0.059 40.6 5.6 47299 47299 -3 13
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 91.4 0.441 0.441 2.4 3.2 2131
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 1.25 34.79 44862 44862 2386 99.14 0.13478 0.13478 0.13317 0.133 0.16544 0.1645 RANDOM 18.013
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] 0.1 0.05 -0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.395 r_dihedral_angle_4_deg 16.613 r_dihedral_angle_3_deg 12.041 r_sphericity_bonded 8.702 r_rigid_bond_restr 7.467 r_dihedral_angle_1_deg 5.369 r_angle_other_deg 1.984 r_angle_refined_deg 1.725 r_chiral_restr 0.114 r_bond_refined_d 0.016
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.395 r_dihedral_angle_4_deg 16.613 r_dihedral_angle_3_deg 12.041 r_sphericity_bonded 8.702 r_rigid_bond_restr 7.467 r_dihedral_angle_1_deg 5.369 r_angle_other_deg 1.984 r_angle_refined_deg 1.725 r_chiral_restr 0.114 r_bond_refined_d 0.016 r_gen_planes_other 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.002 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 1237 Nucleic Acid Atoms Solvent Atoms 284 Heterogen Atoms 57
Software Software Software Name Purpose HKL-3000 phasing REFMAC refinement Coot model building HKL-3000 data reduction HKL-3000 data scaling