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Crystal structure of the bacterial ribosome from Escherichia coli in complex with gentamicin and ribosome recycling factor (RRF).
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2AVY 2AVY,2AW4,2AW7,2AWB experimental model PDB 2AW4 2AVY,2AW4,2AW7,2AWB experimental model PDB 2AW7 2AVY,2AW4,2AW7,2AWB experimental model PDB 2AWB 2AVY,2AW4,2AW7,2AWB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 batch 7.5 277 MPD, PEG 8000, MgCl2, NH4Cl, spermine, spermidine, TRIS, EDTA, pH 7.5, batch, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.36 63.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 208.54 α = 90 b = 378.887 β = 90 c = 736.902 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 93 CCD ADSC QUANTUM 315 2006-10-01 M SINGLE WAVELENGTH 2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 12.3.1 1.111 ALS 12.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 4 139 79.2 0.083 12.1 3.2 382905
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 4 4.4 32.6 0.287 2.2 1.5
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT 2AVY,2AW4,2AW7,2AWB 4 40 437560 382478 18859 87.4 0.261 0.2315 0.305 0.2693
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_deg 0.952 c_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 18536 Nucleic Acid Atoms 32831 Solvent Atoms 300 Heterogen Atoms 91
Software Software Software Name Purpose CNS refinement PDB_EXTRACT data extraction ADSC data collection DENZO data reduction SCALEPACK data scaling CNS phasing