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Crystal structure of the aminoglycoside phosphotransferase APH(3')-Ia, with substrate kanamycin and small molecule inhibitor pyrazolopyrimidine PP1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4EJ7 PDB ENTRY 4EJ7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 298 0.1 M sodium acetate, 18% PEG3350, 2% DMSO, 2 mM kanamycin, 3 mM PP1, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.35 47.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.571 α = 61.12 b = 94.217 β = 73.09 c = 96.878 γ = 87.44
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 300 mm plate BERYLLIUM LENSES 2010-12-02 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 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 1.89 20 97.8 0.047 27.48 3.1 132466 -2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.89 1.92 96.5 0.337 3.024 3.1
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 PDB ENTRY 4EJ7 1.89 19.969 0.13 128187 1972 94.57 0.1543 0.1536 0.1553 0.2042 0.2056
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] 20.3554 -0.9489 1.2442 8.7214 1.974 9.3457
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.469 f_angle_d 1.131 f_chiral_restr 0.074 f_bond_d 0.007 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12576 Nucleic Acid Atoms Solvent Atoms 1404 Heterogen Atoms 335
Software Software Software Name Purpose HKL-3000 data collection PHENIX model building PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing