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The oxazolidinone antibiotics perturb the ribosomal peptidyl-transferase center and effect tRNA positioning
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZJR PDB ENTRY 2ZJR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.8 10mM MgCl2, 60mM NH4Cl, 5mM KCl, 10mM HEPES, pH7.8, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 4.43 72.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 169.7 α = 90 b = 410 β = 90 c = 695 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 100 CCD MAR CCD 165 mm M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA
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 30 90.5 0.133 8.2 272947 34.3
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 3.5 3.77 80.2 0.455 1.9 45746
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 PDB ENTRY 2ZJR 3.5 29.98 -3 272947 13534 90.5 0.259 0.259 0.2671 0.28 0.3072 RANDOM 42.7
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] -3.39 5.85 -2.46
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 19.6 c_improper_angle_d 1.73 c_angle_deg 1.5 c_bond_d 0.01 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 19.6 c_improper_angle_d 1.73 c_angle_deg 1.5 c_bond_d 0.01 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot c_mcbond_it c_mcangle_it c_scbond_it c_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 23347 Nucleic Acid Atoms 60249 Solvent Atoms Heterogen Atoms 61
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling CNS phasing