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Trypanosoma brucei Seryl-tRNA Synthetase in Complex with 5'-O-(N-(L-seryl)-Sulfamoyl)uridine
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)uridine in crystallization solution containing a 22% v/v glycerol.
Crystal Properties Matthews coefficient Solvent content 3.46 64.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 177.609 α = 90 b = 177.609 β = 90 c = 246.109 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 2018-11-20 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 1.84 130.43 98.8 0.082 0.086 0.026 0.998 27.7 10.7 127755 16.12
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 1.84 1.94 91.9 0.419 0.449 0.152 0.969 9.2
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 1.84 21.2 125223 2217 96.9 0.213 0.213 0.1868 0.239 0.2121 RANDOM 24.94
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] 2.7026 2.7026 -5.4052
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.21 t_omega_torsion 3.81 t_angle_deg 1.04 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 15.21 t_omega_torsion 3.81 t_angle_deg 1.04 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 7032 Nucleic Acid Atoms Solvent Atoms 793 Heterogen Atoms 135
Software Software Software Name Purpose BUSTER refinement XDS data reduction Aimless data scaling PDB_EXTRACT data extraction PHASER phasing