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Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with hygromycin A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 292 HEPES, sodium hydroxide, magnesium chloride, ammonium chloride, 2-mercaptoethanol, spermidine, 2-ethyl-1,3-hexanediol, ethanol
Crystal Properties Matthews coefficient Solvent content 4.48 72.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 169.82 α = 90 b = 411.54 β = 90 c = 695.65 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 PIXEL PSI PILATUS 6M 2012-09-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.00001 SLS X06SA
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 3 59.03 99.5 0.215 6.28 4.6 479454 -3
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 3 3.16 99.1 5.623 0.33 4.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3 57.02 1.33 442730 21366 91.9 0.2859 0.2839 0.2689 0.3255 0.3147 142.3831
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] -34.6008 66.1499 -31.5491
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 18.407 f_angle_d 1.215 f_chiral_restr 0.076 f_bond_d 0.009 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 26865 Nucleic Acid Atoms 62274 Solvent Atoms Heterogen Atoms 222
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHENIX phasing Coot model building PHENIX refinement PDB_EXTRACT data extraction