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Structure of N-3 aminoglycoside acetyltransferase XIa (AAC(3)-XIa) in complex with acetylamino coenzyme A and gentamicin
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 2.07 40.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.372 α = 90 b = 100.626 β = 106.624 c = 39.177 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 DECTRIS PILATUS 6M 2021-06-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.97741 ALS 5.0.1
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 1.37 37.54 97.38 0.998 18.76 3.2 53576 15.39
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 1.37 1.419 0.956
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 1.37 37.54 1.43 53553 1454 97.39 0.1632 0.1625 0.1618 0.1901 0.1897 22.66
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 26.1667 f_angle_d 1.7361 f_chiral_restr 0.1035 f_bond_d 0.0162 f_plane_restr 0.0149
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2253 Nucleic Acid Atoms Solvent Atoms 260 Heterogen Atoms 139
Software Software Software Name Purpose PHENIX refinement xia2 data reduction DIALS data scaling PHASER phasing