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High-resolution crystal structure of human SepSecS-tRNASec complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HL2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.4 285 0.24 M lithium citrate, 10% PEG 3350 0.1 M, sodium cacodylate trihydrate, 2.0 mg/mL SepSecS mixed with 0.5 mg/mL tRNASec 2 VAPOR DIFFUSION, SITTING DROP 6.2 285 0.24 M lithium citrate, 9% PEG 3350, 0.1 M sodium cacodylate trihydrate, 6.0 mg/mL SepSecS mixed with 1.5 mg/mL tRNASec
Crystal Properties Matthews coefficient Solvent content 3.7 66.8 3.7 66.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 167.058 α = 90 b = 167.058 β = 90 c = 239.846 γ = 120
Symmetry Space Group P 31 1 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 CCD MARMOSAIC 300 mm CCD 2013-08-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.32 50 99.9 0.133 0.144 0.053 7.9 7.1 165776
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.32 2.36 99.6 1.501 1.704 0.789 0.403 4.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation 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 THROUGHOUT 3HL2 2.32 41.6 1.33 164650 1945 99.86 0.1763 0.176 0.1761 0.2025 0.2024 47.468
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 12.067 f_angle_d 0.619 f_chiral_restr 0.071 f_plane_restr 0.005 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14141 Nucleic Acid Atoms 1783 Solvent Atoms 1311 Heterogen Atoms 112
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PDB_EXTRACT data extraction PHASER phasing