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Crystal structure of human ThrRS complexing with obafluorin derived inhibitor OB-D4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4P3N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 291.15 0.03 M magnesium chloride hexahydrate, 0.03 M calcium chloride dihydrate, 0.045M imidazole, 0.055M MES monohydrate acid pH 6.5, 20% v/v glycol, 10% w/v PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.48 50.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.422 α = 90 b = 73.422 β = 90 c = 356.353 γ = 90
Symmetry Space Group P 41 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 PILATUS3 6M 2025-03-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.979460 SSRF BL18U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 3.5 49.84 100 0.195 0.997 20.4 23.7 13254
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.5 3.83 0.409 0.983
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 3.5 49.84 1.34 13172 1317 99.97 0.2185 0.2121 0.2127 0.2768 0.2739
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 5.873 f_angle_d 0.569 f_chiral_restr 0.043 f_plane_restr 0.004 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6536 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 52
Software Software Software Name Purpose PHENIX refinement Aimless data scaling PHASER phasing PDB_EXTRACT data extraction