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Crystal structure of NLRP3 in complex with inhibitor NP3-562
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 7 298 protein: well = 1: 1
well: 1.94 M Ammonium citrate pH 7.0
protein: 7 mg/ml protein copurified with 1 uM inhibitor
Crystal Properties Matthews coefficient Solvent content 2.79 55.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.238 α = 90 b = 96.238 β = 90 c = 267.973 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 2018-11-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.00 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim 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 2.8 83.34 100 0.33 0.33 0.34 0.998 11.7 19.1 18959 65.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.87 100 4.6 4.73 0.48 0.8 18.1
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.8 79.58 18959 948 100 0.2265 0.2242 0.2702 0.2361 RANDOM 84.07
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] 0.6338 0.6338 -1.2676
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 20.59 t_omega_torsion 2.5 t_angle_deg 0.86 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 3868 Nucleic Acid Atoms Solvent Atoms 80 Heterogen Atoms 56
Software Software Software Name Purpose BUSTER refinement XDS data reduction XSCALE data scaling PHASER phasing