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Trypanosoma brucei seryl-tRNA synthetase in complex with ATP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LSQ PDB entry 3LSQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 sitting drop vapor diffusion 7 298 1 ul 11 mg/ml protein in SGPP buffer mixed with 0.5 ul 2.4 M sodium malonate; crystal then soaked in 3.4 M sodium malonate (pH 7.0) supplemented with 10 mM ATP for 25 minutes before freezing., sitting drop vapor diffusion, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.39 63.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 175.652 α = 90 b = 175.652 β = 90 c = 248.518 γ = 120
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 2008-03-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.979 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 1.95 50 99.9 0.09 9.1 8 106754 5 37
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) 1.95 2.02 99.6 0.808 1.5 6.4 10577
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 3LSQ 1.95 34.57 106719 5392 99.91 0.169 0.168 0.179 0.195 0.2021 RANDOM 50.159
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] 1.14 0.57 1.14 -1.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.025 r_dihedral_angle_4_deg 14.559 r_dihedral_angle_3_deg 13.065 r_dihedral_angle_1_deg 6.111 r_scangle_it 5.824 r_scbond_it 3.85 r_mcangle_it 3.252 r_mcbond_it 2.07 r_angle_refined_deg 1.331 r_angle_other_deg 0.863
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.025 r_dihedral_angle_4_deg 14.559 r_dihedral_angle_3_deg 13.065 r_dihedral_angle_1_deg 6.111 r_scangle_it 5.824 r_scbond_it 3.85 r_mcangle_it 3.252 r_mcbond_it 2.07 r_angle_refined_deg 1.331 r_angle_other_deg 0.863 r_mcbond_other 0.659 r_chiral_restr 0.082 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7265 Nucleic Acid Atoms Solvent Atoms 341 Heterogen Atoms 77
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing