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NACHT domain of NLRP3 in complex with DFV890
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7ALV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.8 293 protein: 0.2 ul NLRP3 (131-679) at 7 mg/ml in 50mM HEPES pH 7.8, 500mM NaCl, 10% glycerol, 1mM MgCl2, 1mM TCEP, 100uM ADP, and 0.8 mM DFV890 (in DMSO)
wel: 0.2 ul 1.99M NH4 3 citrate
Crystal Properties Matthews coefficient Solvent content 2.74 55.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.238 α = 90 b = 96.238 β = 90 c = 262.701 γ = 120
Symmetry Space Group P 61 2 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 PILATUS 6M 2019-05-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.000 SLS X10SA
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 2.771 83.345 77.5 0.304 0.313 0.071 0.998 9.4 18.8 14845 1.2 67.76
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 2.771 2.968 21.5 3.103 3.192 0.741 0.598 1.5 18.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.771 83.34 14845 706 77.5 0.226 0.2241 0.2231 0.2637 0.2567 RANDOM 58.64
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] -0.3893 -0.3893 0.7787
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 21.26 t_omega_torsion 2.63 t_angle_deg 0.85 t_bond_d 0.007 t_dihedral_angle_d t_gen_planes t_it t_chiral_improper_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3864 Nucleic Acid Atoms Solvent Atoms 76 Heterogen Atoms 55
Software Software Software Name Purpose BUSTER refinement XDS data reduction STARANISO data scaling PHASER phasing