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Leishmania major Tyrosyl-tRNA synthetase in complex with tyrosinol, triclinic crystal form 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3P0H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 1:1:0.5 native protein solution (14 mg/ml LmTyrRS in MSGPP buffer containing 1 mM TCEP and 10 mM tyrosinol): well solutionn (16% PEG 3350, 0.2 M potassium formate pH 7.5): seed stock (1:100 dilution in SGPP buffer); cryoprotected by quick soak in 15% ethylene glycol, 18.75% PEG 3350, 187.5 mM potassium formate pH 7.5, 10mM tyrosinol, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.79 55.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.519 α = 74.47 b = 111.934 β = 80.83 c = 141.043 γ = 77.13
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 325 mm CCD 2009-06-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.97946 SSRL BL9-2
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 2.89 135.13 98.6 0.084 14.118 3.6 72441 -3 76
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.89 3 97.9 1.063 3.5
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 3P0H 2.89 50 72441 3649 98.07 0.2462 0.2438 0.2388 0.293 0.2898 RANDOM 143.308
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] 3.68 -2.29 -0.71 -1.74 0.89 -1.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.782 r_dihedral_angle_3_deg 17.15 r_dihedral_angle_4_deg 14.571 r_dihedral_angle_1_deg 5.413 r_angle_refined_deg 1.05 r_angle_other_deg 0.809 r_chiral_restr 0.057 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.782 r_dihedral_angle_3_deg 17.15 r_dihedral_angle_4_deg 14.571 r_dihedral_angle_1_deg 5.413 r_angle_refined_deg 1.05 r_angle_other_deg 0.809 r_chiral_restr 0.057 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19644 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 50
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection HKL-2000 data reduction HKL-2000 data scaling