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Crystal structure of tryptophanyl-tRNA synthetase from Yersinia pestis CO92
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FI0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 291 0.2 M Ca(oAc)2
0.1 M Tris
20% PEG3000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.35 47.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.099 α = 90 b = 78.15 β = 90 c = 152.176 γ = 90
Symmetry Space Group P 21 21 21
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 ADSC QUANTUM 315r mirrors 2010-04-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9794 APS 19-ID
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 40 99.2 0.077 9.3 5.4 55745 53290 2 2
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 1.98 98.4 0.65 2.8 5.3 2581
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 3FI0 1.95 40 2 2 53040 50347 2693 98.66 0.18 0.16905 0.16707 0.1748 0.20615 0.208 RANDOM 22.724
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] -0.28 0.75 -0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.311 r_dihedral_angle_4_deg 18.84 r_dihedral_angle_3_deg 13.712 r_dihedral_angle_1_deg 5.276 r_scangle_it 4.459 r_scbond_it 2.691 r_mcangle_it 1.661 r_angle_refined_deg 1.42 r_angle_other_deg 0.907 r_mcbond_it 0.893
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.311 r_dihedral_angle_4_deg 18.84 r_dihedral_angle_3_deg 13.712 r_dihedral_angle_1_deg 5.276 r_scangle_it 4.459 r_scbond_it 2.691 r_mcangle_it 1.661 r_angle_refined_deg 1.42 r_angle_other_deg 0.907 r_mcbond_it 0.893 r_mcbond_other 0.235 r_chiral_restr 0.097 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5209 Nucleic Acid Atoms Solvent Atoms 445 Heterogen Atoms 7
Software Software Software Name Purpose SBC-Collect data collection PHASER phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling