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Engineered tyrosyl-tRNA synthetase with the nonstandard amino acid L-4,4-biphenylalanine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YXN PDB entry 2YXN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 298 0.1 M sodium malonate, 18 % PEG 3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.66 53.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.34 α = 90 b = 67.205 β = 102.65 c = 90.682 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 2013-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.977 ALS 5.0.1
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 2.65 50 99 0.074 29.2 7.6 27201 26929 1 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.65 2.74 98.4 0.495 4.65 7.7
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 2YXN 2.65 45 26709 26407 1398 98.87 0.22592 0.2218 0.2256 0.30634 0.2999 RANDOM 58.281
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] -3.61 0.23 2.41 0.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.786 r_dihedral_angle_4_deg 19.721 r_dihedral_angle_3_deg 18.931 r_dihedral_angle_1_deg 8.728 r_long_range_B_refined 6.309 r_long_range_B_other 6.301 r_mcangle_it 4.263 r_mcangle_other 3.962 r_scangle_other 3.849 r_angle_other_deg 3.616
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.786 r_dihedral_angle_4_deg 19.721 r_dihedral_angle_3_deg 18.931 r_dihedral_angle_1_deg 8.728 r_long_range_B_refined 6.309 r_long_range_B_other 6.301 r_mcangle_it 4.263 r_mcangle_other 3.962 r_scangle_other 3.849 r_angle_other_deg 3.616 r_mcbond_it 2.544 r_mcbond_other 2.541 r_scbond_it 2.46 r_scbond_other 2.303 r_angle_refined_deg 1.53 r_chiral_restr 0.086 r_bond_refined_d 0.012 r_gen_planes_other 0.008 r_gen_planes_refined 0.006 r_bond_other_d r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6038 Nucleic Acid Atoms Solvent Atoms 57 Heterogen Atoms 13
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling