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Crystal structure of Glutamate-tRNA synthetase GluRS from Chlamydia pneumoniae (Orthorhombic C form)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9Y81
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 291 0.1M NaCH3COO/CH3COOH pH 5.0, 2% PEG 4000, 15% MPD. ChpnA.01348.a.UX11.PS38780 at 8 mg/mL. 2 mM ATP added to the protein prior to crystallization. plate 20340 E8 drop 1, Puck: PSL-1216, Cryo: 25% MPD + 75% crystallant
Crystal Properties Matthews coefficient Solvent content 3.26 62.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.368 α = 90 b = 135.411 β = 90 c = 111.9 γ = 90
Symmetry Space Group C 2 2 21
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 EIGER2 XE 9M 2025-09-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 19-ID 0.9786 NSLS-II 19-ID
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 2.75 47.29 100 0.211 0.227 0.083 0.995 7.4 7.5 20966
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 2.75 2.9 100 1.583 1.695 0.599 0.756 7.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.75 47.29 1.34 20912 1030 99.8 0.2217 0.2194 0.2225 0.2648 0.2713
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 17.265 f_angle_d 0.7 f_chiral_restr 0.04 f_plane_restr 0.006 f_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3852 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 3
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing PDB_EXTRACT data extraction