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Inhibiting peptidylarginine 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 3APM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 protein at 4 mg/mL in buffer 10 mM Tris pH 8.5, 500 mM NaCl, 1 mM DTT, and 1 mM EDTA, and well solution composed of 0.2 M sodium malonate pH 7 and 6% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.69 54.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 143.731 α = 90 b = 59.733 β = 122.441 c = 111.149 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 2019-09-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1 APS 17-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 2.44 71.26 91.2 0.084 0.101 0.054 0.997 10 3.3 14773
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 2.441 2.82 69.3 0.729 0.893 0.508 0.559 1.5
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 2.44 71.26 1.37 14771 713 49.41 0.2183 0.2147 0.2149 0.293 0.2936 69.23
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 19.3462 f_angle_d 1.1003 f_chiral_restr 0.055 f_bond_d 0.0093 f_plane_restr 0.0084
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4241 Nucleic Acid Atoms Solvent Atoms 19 Heterogen Atoms 34
Software Software Software Name Purpose PHENIX refinement XDS data reduction STARANISO data scaling PHASER phasing