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Crystal structure of human selenocystine tRNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2TRA PDB ENTRY 2TRA, 6TNA experimental model PDB 6TNA PDB ENTRY 2TRA, 6TNA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.1 293 32% PEG 1500, 0.1M sodium acetate-HCl pH 4.1, 140mM lithium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.81 56.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.949 α = 90 b = 51.573 β = 101.64 c = 81.365 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 90 CCD ADSC QUANTUM 315 monochromator 2008-10-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.000 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 3.1 50 96.7 0.105 0.105 18 5.4 6032 5833 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 3.1 3.21 85.9 0.39 0.39 3.53 5.4 608
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 THROUGHOUT PDB ENTRY 2TRA, 6TNA 3.1 36.13 5965 5781 258 97 0.254 0.254 0.2575 0.314 0.3214 RANDOM 115
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] 5.19 -55.5 -16.71 11.52
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 13 c_improper_angle_d 1.27 c_angle_deg 0.92 c_bond_d 0.005 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 13 c_improper_angle_d 1.27 c_angle_deg 0.92 c_bond_d 0.005 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot c_mcbond_it c_mcangle_it c_scbond_it c_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 1829 Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose CNS refinement ADSC data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing