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Crystal Structure of NLRP3 NACHT domain in complex with a potent inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5IRN pdbid 5irn, 4kxf experimental model PDB 4KXF pdbid 5irn, 4kxf
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 0.1 M Hepes pH 7.5, 1.4M SodiumCitrate
Crystal Properties Matthews coefficient Solvent content 3.4 54.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.18 α = 90 b = 96.18 β = 90 c = 262.54 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 2018-02-26 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 2.83 79.394 100 0.255 0.289 0.06 0.999 12.9 18.7 12189 88.23
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.835 3.147 13.1 2.366 0.55 0.706 1.7 18
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 pdbid 5irn, 4kxf 2.835 79.39 12189 633 68.2 0.2154 0.2128 0.2257 0.2647 0.2861 RANDOM 83.37
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] 1.4564 1.4564 -2.9129
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 20.01 t_omega_torsion 2.74 t_angle_deg 1 t_bond_d 0.009 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 20.01 t_omega_torsion 2.74 t_angle_deg 1 t_bond_d 0.009 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3718 Nucleic Acid Atoms Solvent Atoms 8 Heterogen Atoms 56
Software Software Software Name Purpose BUSTER refinement STARANISO data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing