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Crystal structure of aminoglycoside nucleotidylyltransferase ANT(2")-Ia, kanamycin-bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4WQK apoprotein
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 60 mg/mL protein, 10% 2-propanol, 20% PEG 4K, 0.1 M HEPES pH 7.5, 15 mM kanamycin B (5:1 molar ratio kanamycin B:protein)
Crystal Properties Matthews coefficient Solvent content 2.21 44.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.46 α = 90 b = 42.01 β = 105.25 c = 47.81 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 IMAGE PLATE RIGAKU RAXIS IV++ 2014-08-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.548
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 1.73 25 99.5 0.064 33.4 2.3 35472 -2 19.44
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 1.73 1.76 100 0.564 3.57 4.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE apoprotein 1.73 23.463 1.35 35415 1784 99.37 0.1495 0.1477 0.1512 0.184 0.1879 Random selection 27.17
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 13.553 f_angle_d 1.668 f_chiral_restr 0.101 f_bond_d 0.02 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1385 Nucleic Acid Atoms Solvent Atoms 236 Heterogen Atoms 83
Software Software Software Name Purpose HKL-3000 data reduction HKL-3000 data scaling PHENIX phasing Coot model building PHENIX refinement