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Crystal structure of apo Tyrosine-tRNA ligase mutant protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1J1U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.1 289 protein sample (40mg/ml) in 25mM Tris-Cl PH8.0, 50mM NaCl mixed with equal volume of reservior solution containing 20-22% PEG3350, 0.2M (NH4)2SO4, 0.1M sodium citrate PH6.1-6.2, for 5 days, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.4 48.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.695 α = 90 b = 38.886 β = 90.98 c = 83.061 γ = 90
Symmetry Space Group P 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 90 CCD MARMOSAIC 225 mm CCD 2010-06-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.979 SSRF BL17U
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 2.29 50 94.8 0.053 30.4 5 15316 14520 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 2.3 2.38 70.5 0.265 4.97 4.3
Refinement Statistics Diffraction ID Structure Solution 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT 1J1U 2.298 31.287 14520 14240 715 92.95 0.2314 0.229 0.2283 0.2766 0.2685
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] -11.0996 -6.925 8.8821 2.2175
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.707 f_angle_d 0.662 f_chiral_restr 0.041 f_bond_d 0.002 f_plane_restr 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2461 Nucleic Acid Atoms Solvent Atoms 3 Heterogen Atoms 14
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing PHASER phasing PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling