☰ Navigation Tabs
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 = 114.092 α = 90 b = 84.023 β = 102.38 c = 134.561 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 3.2 50 99 0.098 38861 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.2 3.42 99.4
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 3.2 44.28 38861 2053 99.13 0.23801 0.23521 0.2263 0.29043 0.279 RANDOM 131.197
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 r_dihedral_angle_2_deg 35.675 r_dihedral_angle_3_deg 21.338 r_dihedral_angle_4_deg 15.84 r_dihedral_angle_1_deg 5.312 r_angle_refined_deg 1.121 r_scangle_it 0.354 r_nbtor_refined 0.303 r_scbond_it 0.218 r_nbd_refined 0.204 r_symmetry_vdw_refined 0.172
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.675 r_dihedral_angle_3_deg 21.338 r_dihedral_angle_4_deg 15.84 r_dihedral_angle_1_deg 5.312 r_angle_refined_deg 1.121 r_scangle_it 0.354 r_nbtor_refined 0.303 r_scbond_it 0.218 r_nbd_refined 0.204 r_symmetry_vdw_refined 0.172 r_xyhbond_nbd_refined 0.145 r_symmetry_hbond_refined 0.137 r_mcangle_it 0.118 r_mcbond_it 0.093 r_chiral_restr 0.07 r_metal_ion_refined 0.027 r_bond_refined_d 0.007 r_gen_planes_refined 0.002 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_mcbond_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 1540 Solvent Atoms Heterogen Atoms 120
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing