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The crystal structure of the 50S Large ribosomal subunit from Deinococcus radiodurans complexed with a short substrate analog ACCPuromycin (ACCP)
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 7.8 ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL;
SOAKING CRYSTALS IN: 0.0125mM ACCP, pH 7.80
Crystal Properties Matthews coefficient Solvent content 4 64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 169.9 α = 90 b = 410.4 β = 90 c = 697.1 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 ADSC QUANTUM 4 2001-02-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 3.5 50 97.8 0.156 7.9 249369 -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) 3.7 3.76 97.3 0.393 1.8
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION DIFFERENCE FOURIER MAPS THROUGHOUT PDB ENTRY 1NKW 3.7 15 240738 240738 12015 0.2831 0.283 0.297 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 0.8 c_angle_deg 0.8 c_bond_d 0.004 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 Nucleic Acid Atoms 59455 Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling CCP4 model building CNS refinement CCP4 phasing O model building