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Pseudomonas aeruginosa Seryl-tRNA Synthetase in Complex with 5'-O-(N-(L-seryl)-sulfamoyl)cytidine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DQ3 Model generated using 2DQ3 as a template
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 Holo protein, concentrated to 10 mg/mL in 10 mM Tris pH 7, 100 mM NaCl, 5mM DTT, was mixed with an equal volume of 100 mM Tris pH 8, 200 mM NaCl, 23% w/v PEG 3350 and 5% v/v ethylene glycol. Suitable crystals were soaked with 2 mM 5'-O-(N-(L-seryl)-sulfamoyl)N3-cytidine in a solution similar to the crystallization condition but containing 22% v/v ethylene glycol.
Crystal Properties Matthews coefficient Solvent content 2.9 57.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 151.006 α = 90 b = 122.183 β = 114.67 c = 65.489 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2017-12-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.972422 ESRF ID23-1
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 2.1 91.25 99.3 0.056 0.067 0.036 0.998 11.7 3.4 62738 51
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 2.1 2.21 99.5 0.605 0.713 0.374 0.752 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 Model generated using 2DQ3 as a template 2.16 43.2 57272 2239 99.1 0.188 0.187 0.1805 0.215 0.2073 RANDOM 52.69
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] -8.9641 2.1753 4.0054 4.9586
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.19 t_omega_torsion 3.55 t_angle_deg 1.07 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 16.19 t_omega_torsion 3.55 t_angle_deg 1.07 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 6089 Nucleic Acid Atoms Solvent Atoms 343 Heterogen Atoms 80
Software Software Software Name Purpose XDS data reduction Aimless data scaling BUSTER refinement PDB_EXTRACT data extraction PHASER phasing