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The crystal structure of the 50S Large ribosomal subunit from Deinococcus radiodurans complexed with a tRNA acceptor stem mimic (ASM) and the antibiotic sparsomycin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NKW PDB ENTRY 1NKW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL,
SPARSOMYCIN; SOAKING CRYSTALS IN: 0.025mM ASM
Crystal Properties Matthews coefficient Solvent content 4 64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 169.6 α = 90 b = 409.4 β = 90 c = 695.1 γ = 90
Symmetry Space Group I 2 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 90 CCD CUSTOM-MADE 2001-11-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID APS 19-ID
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 3.6 50 94.2 0.169 5.8 290998 -3
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 3.6 3.66 93.8 0.356 1.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION DIFFERENCE FOURIER MAPS THROUGHOUT PDB ENTRY 1NKW 3.6 15 250710 250710 12535 0.2841 0.2841 0.284 0.308 random
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 c_angle_d 0.98 c_angle_deg 0.98 c_bond_d 0.007 c_dihedral_angle_d c_improper_angle_d c_mcbond_it c_mcangle_it c_scbond_it c_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 347 Nucleic Acid Atoms 59902 Solvent Atoms Heterogen Atoms 22
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling CCP4 model building CNS refinement CCP4 phasing