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Evolutionary gain of alanine mischarging to non-cognate tRNAs with a G4:U69 base pair
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HXU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 289 0.1 M Hepes pH 7.5, 20% Polyethylene glycol 3350, 0.2 M MgCl2
Crystal Properties Matthews coefficient Solvent content 2.55 51.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.167 α = 90.07 b = 98.26 β = 89.95 c = 201.385 γ = 90.11
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2012-11-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 1.1271 SSRL BL11-1
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 2.68 50 99.2 0.142 5.5 6.9 100341
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.68 2.73 88.7 0.408 0.894 6.8
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 3HXU 2.68 49.13 100341 5119 93.42 0.2179 0.216 0.2839 0.2542 0.3165 RANDOM 55.755
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] -10.09 5.36 -19.53 -1.42 -27.27 11.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.608 r_dihedral_angle_4_deg 18.377 r_dihedral_angle_3_deg 17.603 r_mcangle_it 6.913 r_dihedral_angle_1_deg 6.595 r_mcbond_it 4.478 r_mcbond_other 4.478 r_angle_other_deg 3.151 r_angle_refined_deg 1.996 r_chiral_restr 0.122
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.608 r_dihedral_angle_4_deg 18.377 r_dihedral_angle_3_deg 17.603 r_mcangle_it 6.913 r_dihedral_angle_1_deg 6.595 r_mcbond_it 4.478 r_mcbond_other 4.478 r_angle_other_deg 3.151 r_angle_refined_deg 1.996 r_chiral_restr 0.122 r_bond_other_d 0.02 r_bond_refined_d 0.016 r_gen_planes_other 0.016 r_gen_planes_refined 0.015
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 28360 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 224
Software Software Software Name Purpose HKL-2000 data collection HKL-2000 data scaling REFMAC refinement PDB_EXTRACT data extraction