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Structure of N-3 aminoglycoside acetyltransferase XI (AAC(3)-XI) in complex with coenzyme A, and one apo monomer
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9MGT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 294.15 0.1M Sodium acetate pH 4.6, 10-45% (v/v) 2-methyl-2,4-pentanediol, 0-20% (v/v) PEG 400
Crystal Properties Matthews coefficient Solvent content 1.96 37.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.232 α = 90 b = 99.9 β = 106.87 c = 38.96 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL Bruker PHOTON II 2021-05-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 LIQUID ANODE BRUKER METALJET 1.3418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 2.08 29.88 99.41 0.993 15.68 9.5 15419
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.08 2.154 0.924
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.08 29.88 1.36 15419 2972 97.51 0.1667 0.1626 0.163 0.2023 0.2018
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.474 f_angle_d 0.568 f_chiral_restr 0.043 f_plane_restr 0.005 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2226 Nucleic Acid Atoms Solvent Atoms 136 Heterogen Atoms 53
Software Software Software Name Purpose PHENIX refinement PROTEUM PLUS data reduction PROTEUM PLUS data scaling PHASER phasing