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Crystal Structure of ANT(2")-Ia in complex with adenylyl-2"-tobramycin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4XJE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 295 100 mM sodium acetate pH 4.5, 22% 1,4- butanediol, 1mM MnCl2, 10 mM ATP, 10mM tobramycin
Crystal Properties Matthews coefficient Solvent content 2.25 45.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.09 α = 90 b = 41.91 β = 105.08 c = 47.13 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 93 CCD RIGAKU SATURN 944+ 2x2 binning 2015-02-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.541780
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 1.82 30.83 99.7 0.07 0.016 41.8 19.8 15735 18.29
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.82 1.87 96.5 0.627 0.216 3.8 9.8 1111
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 4XJE 1.82 30.828 1.37 15725 802 99.7 0.1394 0.1376 0.1517 0.1724 0.1837 Random selection 25.6569
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 15.569 f_angle_d 1.284 f_chiral_restr 0.044 f_bond_d 0.009 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1379 Nucleic Acid Atoms Solvent Atoms 213 Heterogen Atoms 92
Software Software Software Name Purpose PHENIX refinement StructureStudio data collection xia2 data scaling XDS data reduction XSCALE data scaling PHASER phasing PDB_EXTRACT data extraction