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Crystal structure of the aminoglycoside phosphotransferase APH(3')-Ia, with substrate kanamycin and small molecule inhibitor 1-NM-PP1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4EJ7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 298 0.1 M SODIUM ACETATE, 8% PEG3350, 3% DMSO, 2 MM KANAMYCIN, 3 mM 1-NM-PP1, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.3 46.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.843 α = 103.24 b = 97.103 β = 106.18 c = 112.128 γ = 112.66
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 300 mm CCD 2012-04-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.88 99.63 97.6 0.062 7.6 2.3 265977 -2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.88 1.98 96.5 0.372 2.1 2.3
Refinement Statistics Diffraction ID Structure Solution Method Starting model 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 4EJ7 1.88 54.384 1.96 248673 12522 94.43 0.1681 0.1655 0.1679 0.2158 0.2178
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 13.249 f_angle_d 1.159 f_chiral_restr 0.076 f_bond_d 0.008 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 25493 Nucleic Acid Atoms Solvent Atoms 3308 Heterogen Atoms 865
Software Software Software Name Purpose HKL-3000 data collection PHENIX model building PHENIX refinement XDS data reduction SCALA data scaling PHENIX phasing