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2'-Trifluoromethylthiouridine-modified E. coli 23S rRNA Sarcin Ricin Loop
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DVZ PDB ENTRY 3DVZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 3.2 M ammonium sulfate, 50 mM potassium MOPS, pH 7.0, 10 mM magnesium chloride, 10 mM manganese chloride, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.9 35.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 29.56 α = 90 b = 29.56 β = 90 c = 76.73 γ = 90
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 2M 2013-11-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.0 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.158 29.56 99.3 17.8 12.1 22865 22732 -3 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.158
Refinement Statistics Diffraction ID Structure Solution 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 3DVZ 1.158 29.56 1.4 22731 1137 99.41 0.117 0.1154 0.1174 0.1481 0.152
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 12.895 f_angle_d 1.74 f_chiral_restr 0.071 f_plane_restr 0.023 f_bond_d 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 583 Solvent Atoms 130 Heterogen Atoms 11
Software Software Software Name Purpose MOLREP phasing PHENIX refinement XDS data reduction XDS data scaling