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Co-crystal structure of PA3774 bound to a trifluoromethyl oxadiazole inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5G0Y Using the A chain of PA3774 for modeling
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.6 293.15 ** Crystallized construct:**
-Contains: UniProt Q9HXM1 (1-380) + C-terminal VDAL residues (381-384).
**Crystallization:**
- Reservoir solution:
1.0 M K2HPO4,
1.0 M NaH2PO4,
0.1 M (NH4)2SO4,
pH 7.6
- Temperature: 291.15 K
- Cryoprotection: 16% (v/v) glycerol added directly to crystal mother liquor
- Cryocooling: Flash-cooled in liquid nitrogen without additional soaking
Crystal Properties Matthews coefficient Solvent content 2.12 41.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.487 α = 90 b = 81.487 β = 90 c = 205.238 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 CCD ADSC QUANTUM 315r 2022-09-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.9791 SSRF BL18U1
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 1.499 43.4191 99.9129 0.08 4.84 12.65 111256
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 1.4993 1.661 99.7 0.9999
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 1.499 43.419 1.36 111256 5563 99.91 0.1865 0.1853 0.1942 0.2088 0.2155
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 16.667 f_angle_d 1.056 f_chiral_restr 0.074 f_bond_d 0.009 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5669 Nucleic Acid Atoms Solvent Atoms 133 Heterogen Atoms 72
Software Software Software Name Purpose PHENIX refinement XDS data reduction PHASER phasing Coot model building XSCALE data scaling