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Seryl-tRNA synthetase in complex with a fragment-sized inhibitor (3-cyclopropyl benzoic acid)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6R1M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 HEPES pH 7.5 0.1 M, PEG Smear Medium 25% (w/v), Glycerol 20% (w/v)
Crystal Properties Matthews coefficient Solvent content 3.15 60.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.196 α = 90 b = 91.196 β = 90 c = 127.059 γ = 120
Symmetry Space Group P 31 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 EIGER2 XE 16M 2025-08-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9406 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.468 49.5 99.9 0.081 20.7 104619 23.13
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.468 1.493 100 0.359
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 1.47 49.5 1.33 104619 5170 99.91 0.1727 0.1714 0.1771 0.198 0.2014 33.58
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 16.5687 f_angle_d 0.76 f_chiral_restr 0.0695 f_plane_restr 0.0077 f_bond_d 0.0047
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3221 Nucleic Acid Atoms Solvent Atoms 152 Heterogen Atoms 18
Software Software Software Name Purpose PHENIX refinement autoPROC data reduction Aimless data scaling PHASER phasing