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Crystal structure of a GNAT superfamily acetyltransferase PA4794 in complex with 4-methylumbelliferyl phosphate
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 48.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.34 α = 90 b = 76.486 β = 90 c = 39.336 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 2010-07-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9794 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 1.3 39.37 99.5 0.055 0.055 48.9 6.1 43284 43284 -3 16.4
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 92.8 0.516 0.516 2.8 4.6 1978
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 39.37 40968 40968 2167 99.5 0.12395 0.12395 0.12242 0.1239 0.15198 0.1531 RANDOM 19.999
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] -0.27 -0.62 0.89
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 38.644 r_dihedral_angle_2_deg 35.821 r_dihedral_angle_4_deg 17.403 r_rigid_bond_restr 14.594 r_sphericity_bonded 14.11 r_dihedral_angle_3_deg 11.728 r_dihedral_angle_1_deg 5.563 r_angle_other_deg 3.593 r_angle_refined_deg 1.842 r_chiral_restr 0.116
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 38.644 r_dihedral_angle_2_deg 35.821 r_dihedral_angle_4_deg 17.403 r_rigid_bond_restr 14.594 r_sphericity_bonded 14.11 r_dihedral_angle_3_deg 11.728 r_dihedral_angle_1_deg 5.563 r_angle_other_deg 3.593 r_angle_refined_deg 1.842 r_chiral_restr 0.116 r_bond_refined_d 0.017 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_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1240 Nucleic Acid Atoms Solvent Atoms 239 Heterogen Atoms 96
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