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Crystal Structure of NLRP3 NACHT domain in complex with NP3-1
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 291 23~25 % w/v Polyethylene glycol monomethyl ether 5,000 ;100 mM MES pH 6.3~6.7 ;200 mM Ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.73 54.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.246 α = 90 b = 97.246 β = 90 c = 256.792 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 PILATUS3 6M 2024-01-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 1 SPring-8 BL45XU
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 3.32 84.22 60.1 0.77 0.78 0.127 0.992 6 36.5 6782
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 3.32 3.797 9.5 2.702 2.745 0.468 0.749 1.8
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 3.32 84.22 6434 348 60.1 0.30687 0.30474 0.3095 0.34679 0.3497 RANDOM 83.869
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] 0.54 0.27 0.54 -1.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.425 r_dihedral_angle_3_deg 14.257 r_dihedral_angle_4_deg 10.488 r_dihedral_angle_1_deg 6.728 r_long_range_B_refined 4.761 r_long_range_B_other 4.76 r_mcangle_it 1.667 r_mcangle_other 1.666 r_angle_refined_deg 1.507 r_angle_other_deg 1.266
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.425 r_dihedral_angle_3_deg 14.257 r_dihedral_angle_4_deg 10.488 r_dihedral_angle_1_deg 6.728 r_long_range_B_refined 4.761 r_long_range_B_other 4.76 r_mcangle_it 1.667 r_mcangle_other 1.666 r_angle_refined_deg 1.507 r_angle_other_deg 1.266 r_scangle_other 0.916 r_mcbond_it 0.887 r_mcbond_other 0.887 r_scbond_it 0.436 r_scbond_other 0.436 r_chiral_restr 0.071 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3910 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 60
Software Software Software Name Purpose autoPROC data reduction STARANISO data scaling PHASER phasing REFMAC refinement