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tRNA-dihydrouridine synthase from Thermus thermophilus in complex with tRNA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 Tris-HCl, ammonium sulfate, glycerol, pH 7-8, vapor diffusion, sitting drop, temperature 293K
Crystal Properties Matthews coefficient Solvent content 4.28 71.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.89 α = 90 b = 118.89 β = 90 c = 319.55 γ = 90
Symmetry Space Group P 41 21 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 ADSC QUANTUM 315 2010-04-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 0.97881 Photon Factory BL-5A
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 3.51 48.605 99.5 0.116 17.1 13.2 29454 29454
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.51 3.7 97.1 0.531 0.531 0.555 0.158 4.6 11.8 4077
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 3.51 48.6 29334 2326 99.3 0.3 0.3011 0.32 0.3192 RANDOM 148.8284
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] 31.45 31.45 -62.89
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.3 c_scangle_it 2.93 c_improper_angle_d 2.88 c_mcangle_it 2.8 c_scbond_it 1.83 c_mcbond_it 1.61 c_angle_deg 0.9 c_bond_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5020 Nucleic Acid Atoms 3122 Solvent Atoms Heterogen Atoms 62
Software Software Software Name Purpose SCALA data scaling CNS refinement PDB_EXTRACT data extraction SERGUI data collection XDS data reduction AutoSol phasing