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tRNA-dihydrouridine synthase from Thermus thermophilus in complex with tRNA fragment
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3B0P PDB ENTRY 3B0P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 HEPES, PEG 12000, pH 7.0, vapor diffusion, sitting drop, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.13 42.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 126.643 α = 90 b = 126.643 β = 90 c = 112.67 γ = 120
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 210 2010-10-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.000 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 1.948 19.798 99.7 0.065 18.4 5.7 49091 49091
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 1.95 2.05 98.6 0.528 0.528 0.582 0.245 3.5 5.6 7132
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 3B0P 1.948 19.798 1.97 49073 2157 99.72 0.1823 0.1806 0.1752 0.2198 0.2167 RANDOM 31.6774
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] -2.8948 -2.8948 5.7895
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.965 f_angle_d 0.683 f_chiral_restr 0.05 f_bond_d 0.006 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4968 Nucleic Acid Atoms 170 Solvent Atoms 418 Heterogen Atoms 62
Software Software Software Name Purpose SCALA data scaling MOLREP phasing PHENIX refinement PDB_EXTRACT data extraction SERGUI data collection XDS data reduction