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Potent inhibition of the protein arginine deiminases (PAD1-4) by targeting a Ca2+ dependent allosteric binding site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4N2B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 protein at 8 mg/mL in buffer 20 mM Tris pH 7.5, 10% glycerol, 500 mM NaCl, 0.5 mM TCEP, and 1 mM EDTA, and well solution composed of 0.1 M magnesium acetate, 50 mM MES pH 5.5, and 9-16%
methyl 2,4-pentane diol
Crystal Properties Matthews coefficient Solvent content 2.39 48.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 201.127 α = 90 b = 51.051 β = 106.28 c = 76.208 γ = 90
Symmetry Space Group C 1 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 EIGER X 16M 2024-09-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.0 APS 17-ID
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 1.77 96.6 92.7 0.05 0.999 14.6 3.3 40310
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 1.77 2.02 0.74 0.722 1.7
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 THROUGHOUT 1.77 96.53 1.35 40305 1899 55.54 0.1869 0.1849 0.1849 0.2271 0.2278
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 12.96 f_angle_d 0.597 f_chiral_restr 0.045 f_plane_restr 0.004 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5110 Nucleic Acid Atoms Solvent Atoms 378 Heterogen Atoms 37
Software Software Software Name Purpose PHENIX refinement XDS data reduction STARANISO data scaling PHASER phasing