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4,5-linked aminoglycoside antibiotics regulate the bacterial ribosome by targeting dynamic conformational processes within intersubunit bridge B2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other IN-HOUSE STRUCTURE CONTAINING ALL RIBOSOMAL PROTEINS IN ONE CHAIN AND RRNA IN ANOTHER
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 6.5 291 PEG8k, MPD, KCl, KSCN
Crystal Properties Matthews coefficient Solvent content 3.2 61.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 212.1 α = 90 b = 435.24 β = 90 c = 614.44 γ = 90
Symmetry Space Group P 21 21 21
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 ADSC QUANTUM 315r 2012-12-03 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD ADSC QUANTUM 315r 2012-10-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.1 ALS 8.3.1 2 SYNCHROTRON ALS BEAMLINE 12.3.1 1.1 ALS 12.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 2.9 70 73.7 0.163 0.178 6.29 914752 -3 73.274
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 3 4.2 1.138 1.592 0.36
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE IN-HOUSE STRUCTURE CONTAINING ALL RIBOSOMAL PROTEINS IN ONE CHAIN AND RRNA IN ANOTHER 3 70 909645 81.14 0.1738 0.1801 0.2534 0.2565 101.9156
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19975 Nucleic Acid Atoms 34942 Solvent Atoms Heterogen Atoms 527
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHENIX phasing PDB_EXTRACT data extraction