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The crystal structure of the large ribosomal subunit of Staphylococcus aureus in complex with telithromycin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4WCE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293.15 Hepes, KCl, MgCl2, NH4Cl, MPD, EtOH, Spermidine
Crystal Properties Matthews coefficient Solvent content 3.8 67.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 282.66 α = 90 b = 282.66 β = 90 c = 877.075 γ = 120
Symmetry Space Group P 65 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 100 PIXEL DECTRIS PILATUS 6M-F 2014-04-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.973 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 3.4 50 98.3 0.165 0.177 0.063 5.7 6.8 268208 114.52
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.4 3.46 94.4 0.492 0.473 4.4 12699
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 THROUGHOUT 4WCE 3.427 50.188 1.35 267947 13517 97.41 0.1939 0.1919 0.1916 0.2315 0.2303 Random selection
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 16.682 f_angle_d 1.106 f_chiral_restr 0.058 f_bond_d 0.006 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19882 Nucleic Acid Atoms 60575 Solvent Atoms Heterogen Atoms 576
Software Software Software Name Purpose PHENIX refinement DENZO data reduction SCALEPACK data scaling PDB_EXTRACT data extraction DNA data collection