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Biphenylalanine modified threonyl-tRNA synthetase from Pyrococcus abyssi: 11BIF, 42F, 79V, and 123A 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 0.1M sodium citrate, 15% PEG 6000, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.72 54.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.43 α = 90 b = 79.15 β = 90 c = 90.74 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 PIXEL DECTRIS PILATUS 6M 2014-03-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.97945 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 2.1 50 97.9 0.092 8.7 4 11066
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 2.1 2.21 99.2 0.389 3.1 4.1 1594
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 1y2q 2.1 50 10543 523 97.39 0.18766 0.1865 0.1787 0.21159 0.1994 RANDOM 34.356
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] -9.64 -1.93 11.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.632 r_dihedral_angle_3_deg 16.612 r_dihedral_angle_4_deg 13.568 r_dihedral_angle_1_deg 7.032 r_long_range_B_refined 6.589 r_long_range_B_other 6.587 r_scangle_other 4.703 r_scbond_it 2.996 r_scbond_other 2.992 r_mcangle_it 2.762
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.632 r_dihedral_angle_3_deg 16.612 r_dihedral_angle_4_deg 13.568 r_dihedral_angle_1_deg 7.032 r_long_range_B_refined 6.589 r_long_range_B_other 6.587 r_scangle_other 4.703 r_scbond_it 2.996 r_scbond_other 2.992 r_mcangle_it 2.762 r_mcangle_other 2.761 r_mcbond_it 2.048 r_mcbond_other 2.041 r_angle_refined_deg 1.768 r_angle_other_deg 0.832 r_chiral_restr 0.106 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_gen_planes_other 0.003 r_bond_other_d 0.001 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 1117 Nucleic Acid Atoms Solvent Atoms 50 Heterogen Atoms 7
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement XDS data scaling