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tRNA processing enzyme complex 3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3WFO 3WFO, 3L0U experimental model PDB 3L0U 3WFO, 3L0U
Crystallization Crystal Properties Matthews coefficient Solvent content 3.69 66.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 177.21 α = 90 b = 148.11 β = 98.54 c = 92.25 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 2012-11-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.97910 Photon Factory BL-17A
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 3.3 20 27238 62.78
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT 3WFO, 3L0U 3.311 19.861 1.99 27165 1363 77.76 0.2311 0.2287 0.23 0.2757 0.2783 113.7954
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 13.073 f_angle_d 0.718 f_chiral_restr 0.034 f_bond_d 0.005 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7021 Nucleic Acid Atoms 3130 Solvent Atoms Heterogen Atoms 20
Software Software Software Name Purpose PHENIX refinement