☰ Navigation Tabs
Crystal structure of a 4-thiouridine synthetase - RNA complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2C5S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.6 292 1 micro-liter of ThiI-RNA complex solution at 10 mg/ml in a buffer consisting of 150 mM ammonium sulfate, 20mM Tris/HCl pH 7.5 was mixed with 3 micro-liter of freshly prepared reservoir solution (2.0 M sodium formate, 100 mM sodium citrate, 2 mMDTT), VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.92 57.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.652 α = 90 b = 110.325 β = 90 c = 119.313 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 100 CCD MAR CCD 165 mm MIRRORS 2006-11-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 BESSY 14.1
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 2.85 30 96.4 0.085 16.42 6.5 30547 -3 60.02
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 2.85 2.95 81.4 0.626 2.06
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 2C5S 2.85 30 1.99 30363 30363 1513 95.9 0.188 0.186 0.187 0.228 0.2277 83.33
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 16.917 f_angle_d 0.927 f_chiral_restr 0.062 f_bond_d 0.012 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6232 Nucleic Acid Atoms 1666 Solvent Atoms 75 Heterogen Atoms 4
Software Software Software Name Purpose XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing