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Biphenylalanine modified threonyl-tRNA synthetase from Pyrococcus abyssi: I11BIF, F42W, Y79A, and F123Y mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Y2Q PDB entry 1y2q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 293 0.1 M sodium citrate, 15% PEG 6000, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.72 54.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.715 α = 90 b = 77.284 β = 90 c = 93.153 γ = 90
Symmetry Space Group I 2 2 2
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 MARMOSAIC 300 mm CCD 2013-11-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.0332 APS 23-ID-B
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 1.95 50 99.5 0.107 16.6 11 14118
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 1.95 2.06 100 0.415 8.1 11.1 2030
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1y2q 1.95 24.1 13408 709 99.12 0.1649 0.16333 0.19595 0.2124 RANDOM 33.616
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] -13.7 2.9 10.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.933 r_dihedral_angle_3_deg 16.191 r_long_range_B_other 8.703 r_long_range_B_refined 8.701 r_dihedral_angle_4_deg 6.705 r_scangle_other 6.102 r_dihedral_angle_1_deg 5.976 r_scbond_it 3.979 r_scbond_other 3.972 r_mcangle_it 3.216
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.933 r_dihedral_angle_3_deg 16.191 r_long_range_B_other 8.703 r_long_range_B_refined 8.701 r_dihedral_angle_4_deg 6.705 r_scangle_other 6.102 r_dihedral_angle_1_deg 5.976 r_scbond_it 3.979 r_scbond_other 3.972 r_mcangle_it 3.216 r_mcangle_other 3.215 r_mcbond_it 2.268 r_mcbond_other 2.254 r_angle_refined_deg 1.797 r_angle_other_deg 0.836 r_chiral_restr 0.105 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 1101 Nucleic Acid Atoms Solvent Atoms 69 Heterogen Atoms 21
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement XDS data scaling