9HG4 | pdb_00009hg4

NACHT domain of NLRP3 in complex with DFV890

X-RAY DIFFRACTION

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.