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Klebsiella pneumoniae 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 2DQ3 Model generated from structure 2DQ3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 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 7.5% w/v PEG 8000, 50 mM CaCl2, 20% v/v ethylene glycol, 100 mM Morpheus buffer system 1 (MES/Imidazole) pH 6.5. Suitable crystals were soaked with 2 mM compound in a similar crystallization solution containing a 10% w/v PEG 8000.
Crystal Properties Matthews coefficient Solvent content 4.2 70.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.321 α = 90 b = 84.321 β = 90 c = 229.998 γ = 90
Symmetry Space Group P 43 21 2
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 2.05 115 99.9 0.08 0.085 0.029 0.999 11.6 8.6 52888 61.63
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 2.05 2.16 99.8 2.089 2.22 0.746 0.73 8.7
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 from structure 2DQ3 2.25 59.62 40368 2036 100 0.211 0.21 0.2014 0.223 0.2157 RANDOM 66.84
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] -8.401 -8.401 16.8019
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.45 t_omega_torsion 3.55 t_angle_deg 1.08 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 17.45 t_omega_torsion 3.55 t_angle_deg 1.08 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 3327 Nucleic Acid Atoms Solvent Atoms 72 Heterogen Atoms 42
Software Software Software Name Purpose XDS data reduction Aimless data scaling BUSTER refinement PDB_EXTRACT data extraction PHASER phasing