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How CCA is added to the 3' end of immature tRNA without the use of an oligonucleotide template
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1R89 PDB entry 1R89
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 295 pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.5 50
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.641 α = 90 b = 84.77 β = 104.66 c = 135.813 γ = 90
Symmetry Space Group P 1 21 1
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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 NSLS X25
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.1 47.7 98.7 0.072 3.1 122568 -3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 1R89 2.2 47.7 122568 6447 99.07 0.19454 0.19207 0.1981 0.24168 0.2418 RANDOM 45.443
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] 0.39 -0.3 0.21 -0.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.431 r_dihedral_angle_4_deg 16.813 r_dihedral_angle_3_deg 16.543 r_dihedral_angle_1_deg 5.465 r_scangle_it 3.329 r_scbond_it 2.45 r_mcangle_it 1.45 r_mcbond_it 1.272 r_angle_refined_deg 1.165 r_angle_other_deg 0.956
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.431 r_dihedral_angle_4_deg 16.813 r_dihedral_angle_3_deg 16.543 r_dihedral_angle_1_deg 5.465 r_scangle_it 3.329 r_scbond_it 2.45 r_mcangle_it 1.45 r_mcbond_it 1.272 r_angle_refined_deg 1.165 r_angle_other_deg 0.956 r_mcbond_other 0.292 r_symmetry_vdw_other 0.212 r_nbd_refined 0.187 r_nbd_other 0.184 r_nbtor_refined 0.184 r_xyhbond_nbd_refined 0.147 r_symmetry_vdw_refined 0.12 r_symmetry_hbond_refined 0.097 r_nbtor_other 0.077 r_metal_ion_refined 0.07 r_chiral_restr 0.066 r_xyhbond_nbd_other 0.032 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_metal_ion_other r_symmetry_hbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14520 Nucleic Acid Atoms 1598 Solvent Atoms 1059 Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing