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Klebsiella pneumoniae Seryl-tRNA synthetase in Complex with Compound SerS7HMDDA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6H9X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 Holo protein at 10 mg/mL in 10 mM Tris pH 7, 100 mM NaCl, 5 mM 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 5 mM synthesized compound in the same crystallization solution but containing a 10% w/v PEG 8000 concentration.
Crystal Properties Matthews coefficient Solvent content 4.23 70.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.67 α = 90 b = 84.67 β = 90 c = 229.865 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 2017-10-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.991870 SOLEIL PROXIMA 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 1.91 19.96 99.8 0.105 0.11 0.032 0.999 10.7 12.2 65882 53.83
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 1.91 2.01 99.6 4.007 4.176 1.17 0.756 12.6
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6H9X 2.18 19.96 44514 2050 100 0.2012 0.2 0.2259 0.2394 RANDOM 61.19
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] -9.5607 -9.5607 19.1215
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.12 t_omega_torsion 3.69 t_angle_deg 0.95 t_bond_d 0.008 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 16.12 t_omega_torsion 3.69 t_angle_deg 0.95 t_bond_d 0.008 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 3310 Nucleic Acid Atoms Solvent Atoms 118 Heterogen Atoms 46
Software Software Software Name Purpose BUSTER refinement XDS data reduction Aimless data scaling PDB_EXTRACT data extraction PHASER phasing