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tRNA-dihydrouridine synthase from Thermus thermophilus
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 HEPES, MgCl2, PEG 4000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.96 37.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.01 α = 76.22 b = 60.19 β = 88.67 c = 67 γ = 70.67
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 270 2010-10-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1.000 Photon Factory AR-NE3A
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 1.7 20 95.6 0.046 17.94 63578 -3 20.35
Refinement Statistics Diffraction ID Structure Solution 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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT 1.7 19.775 1.99 62618 4402 94.33 0.1701 0.1677 0.2024 0.1678 29.86
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] 6.1745 -0.2498 3.9763 -3.2439 0.6503 -2.9306
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.103 f_angle_d 1.084 f_chiral_restr 0.075 f_bond_d 0.008 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4901 Nucleic Acid Atoms Solvent Atoms 387 Heterogen Atoms 62
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction SERGUI data collection XDS data reduction XDS data scaling MOLREP phasing