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Structure of large ribosomal subunit in complex with virginiamycin M
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JJ2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.8 292 1.2M KCl, 0.5M (NH4)Cl, 30mM MgCl2, 8% PEG, pH 5.80,
VAPOR DIFFUSION, SITTING DROP at 292K
Crystal Properties Matthews coefficient Solvent content 3.17 61.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 212.902 α = 90 b = 300.474 β = 90 c = 575.176 γ = 90
Symmetry Space Group C 2 2 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 MARRESEARCH 2000-12-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 1.0332 NSLS X25
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 50 98.7 0.144 0.144 7.7 3.6 344322 339727 -3 33.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 3 3.05 97.7 0.49 0.49 1.7 2.1 16729
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 MOLECULAR REPLACEMENT THROUGHOUT 1JJ2 3 20 346861 327972 3203 94.6 0.2011 0.201 0.242 same reflections as 1JJ2 43.9
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] 5.14 1.7 -6.84
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 15.6 c_scangle_it 2.02 c_mcangle_it 1.84 c_improper_angle_d 1.57 c_angle_deg 1.3 c_scbond_it 1.3 c_mcbond_it 1.12 c_bond_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 28801 Nucleic Acid Atoms 61617 Solvent Atoms 7882 Heterogen Atoms 269
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling CNS refinement CNS phasing