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Leishmania major Tyrosyl-tRNA synthetase in complex with tyrosinol, cubic crystal form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3P0H PDB entry 3P0H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 equal volumes SeMet protein solution (24 mg/ml LmTyrRS in MSGPP buffer containing 5 mM DTT and 10 mM tyrosinol) and well solution (25% PEG 3350, 0.1 M tri-sodium citrate pH 5.5, 10 mM Ferric III Chloride); cryoprotected by addition of 26% PEG 3350, 8% MSGPP buffer, 8% ethylene glycol, 20% glycerol and 0.09 M tri-sodium citrate pH 5.5 directly to drop prior to mounting and freezing crystals in liquid nitrogen, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.8 67.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 241.4 α = 90 b = 241.4 β = 90 c = 241.4 γ = 90
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 2010-03-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.97908 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 3.13 85.35 99.93 0.182 7.3331 7.98 41253 83
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 3.13 3.3 99.82 0.014 6.96
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 FOURIER SYNTHESIS THROUGHOUT PDB entry 3P0H 3.13 85.35 41212 2062 99.81 0.2409 0.2395 0.244 0.2679 0.2685 RANDOM 122.862
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.921 r_dihedral_angle_4_deg 19.718 r_dihedral_angle_3_deg 18.697 r_dihedral_angle_1_deg 5.945 r_angle_refined_deg 1.162 r_angle_other_deg 0.925 r_chiral_restr 0.065 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.921 r_dihedral_angle_4_deg 19.718 r_dihedral_angle_3_deg 18.697 r_dihedral_angle_1_deg 5.945 r_angle_refined_deg 1.162 r_angle_other_deg 0.925 r_chiral_restr 0.065 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.002 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_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it 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 9278 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 24
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection REFMAC phasing