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Crystal structure of tRNA-dihydrouridine(20) synthase dsRBD domain
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 292 Protein 20 mg/mL
precipitant: HEPES 100 mM pH 6.5, sodium acetate 100 mM, PEG 2000 MME 30%
Crystal Properties Matthews coefficient Solvent content 2.12 41.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.13 α = 90 b = 55.13 β = 90 c = 114.66 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 PSI PILATUS 6M 2014-03-17 M SINGLE WAVELENGTH 2 1 x-ray 100 PIXEL PSI PILATUS 6M 2011-09-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 1.000 SOLEIL PROXIMA 1 2 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 1.7712 SOLEIL PROXIMA 1
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 1.7 39.74 99.69 22.06 4.51 38156 38156
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 1.69 1.75 97.65 0.3364 4.16 4.3
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 SAD FREE R-VALUE 1.7 39.738 1.37 37509 1876 99.91 0.1639 0.163 0.1661 0.1802 0.1807
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 14.409 f_angle_d 1.047 f_chiral_restr 0.045 f_bond_d 0.007 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2242 Nucleic Acid Atoms Solvent Atoms 367 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling