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Trypanosoma brucei Seryl-tRNA Synthetase in Complex with 5'-O-(N-(L-seryl)-sulfamoyl)N3-methyluridine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LSQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 Holo protein at 10 mg/mL in 10 mM Tris pH 7, 100 mM NaCl, 5 mM DTT, 5% (v/v) glycerol was mixed with 2.4 M sodium malonate pH 7.0, 100 mM Bis-tris propane pH 7.0 in a 2:1 (v/v) ratio. Suitable crystals were soaked with 2 mM 5'-O-(N-(L-seryl)-sulfamoyl)N3-methyluridine in the crystallization solution containing additional 22% v/v glycerol.
Crystal Properties Matthews coefficient Solvent content 3.55 65.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 177.666 α = 90 b = 177.666 β = 90 c = 246.767 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 IMAGE PLATE MAR scanner 345 mm plate mirrors 2018-03-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.541790
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.9 130.56 99.1 0.103 0.108 0.032 0.999 16.7 11.1 116567 27.75
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 2 97.9 0.803 0.841 0.248 0.874 11
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 3LSQ 1.9 27.54 116513 2336 99 0.174 0.173 0.1651 0.204 0.192 RANDOM 32.2
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] -0.9335 -0.9335 1.867
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 14.88 t_omega_torsion 3.86 t_angle_deg 1 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 14.88 t_omega_torsion 3.86 t_angle_deg 1 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7017 Nucleic Acid Atoms Solvent Atoms 735 Heterogen Atoms 123
Software Software Software Name Purpose BUSTER refinement XDS data reduction Aimless data scaling PDB_EXTRACT data extraction PHASER phasing