8ZGD | pdb_00008zgd

The Crystal Structure of the NLRP1_LRR domain from Biortus.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4IM6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	20mM MgCl2, 0.1M Tris pH 8.0, 19% polyacrylic acid 5100

Crystal Properties
Matthews coefficient	Solvent content
3.06	59.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.582	α = 90
b = 84.582	β = 90
c = 132.495	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 EIGER X 9M		2024-01-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.952989	CLSI	08ID-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.05	49.13	100	0.21	13.5	19.1		18288

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.05	2.11			0.964

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.05	49.13	18236	916	99.962	0.178	0.1757	0.19	0.2209	0.23	22.717

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]
-0.173	-0.087		-0.173		0.562

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.5
r_dihedral_angle_3_deg	12.02
r_lrange_it	9.232
r_lrange_other	9.16
r_dihedral_angle_2_deg	7.628
r_scangle_it	6.761
r_scangle_other	6.758
r_dihedral_angle_1_deg	5.686
r_scbond_it	4.134
r_scbond_other	4.131
r_mcangle_it	4.012
r_mcangle_other	4.012
r_mcbond_it	2.696
r_mcbond_other	2.685
r_angle_refined_deg	1.929
r_angle_other_deg	0.654
r_symmetry_xyhbond_nbd_refined	0.272
r_nbd_refined	0.239
r_xyhbond_nbd_refined	0.198
r_symmetry_xyhbond_nbd_other	0.189
r_symmetry_nbd_other	0.187
r_nbtor_refined	0.174
r_nbd_other	0.134
r_chiral_restr	0.097
r_symmetry_nbd_refined	0.089
r_symmetry_nbtor_other	0.076
r_bond_refined_d	0.009
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1534
Nucleic Acid Atoms
Solvent Atoms	188
Heterogen Atoms	6

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing