4YZ9 | pdb_00004yz9

Crystal Structure of human phosphorylated IRE1alpha in complex with a type III kinase inhibitor (GSK2850163A)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3P23

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	Crystals of pIRE1alpha (547 - 977) with GSK2850163 were prepared by mixing pIRE1alpha with 0.5 mM GSK2850163 and incubating overnight on ice. The crystals were grown at 20 C by vapor diffusion in sitting drops containing 2 ul of protein (13 mg/ml in 50 mM Hepes, pH 7.5, 200 mM NaCl, 5 mM DTT, 1 mM EDTA , 0.5 mM GSK2850163, 0.25% DMSO ) and 2 ul reservoir solution containing PEG 3350 (16%-22%), 100 mM Hepes pH 7.0, 200 mM Ca2+ acetate. The crystals were thick rods that appeared over 2-5 days and reached full size (0.05 X 0.025 X 0.3 mm) in 2 weeks. Seeding was used to improve crystal quality. The pIRE1alpha + GSK2850163 crystals were frozen in a solution of 20% ethylene glycol, 22% PEG 3350, 0.2 M calcium acetate added in a stepwise manner to the protein drop before mounting the crystal on the loop.

Crystal Properties
Matthews coefficient	Solvent content
3.01	59.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 244.004	α = 90
b = 77.767	β = 90
c = 88.313	γ = 90

Symmetry
Space Group	P 21 21 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	CCD	RAYONIX SX-165mm		2011-10-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.45	29.182	97.2	0.073	0.073	9	6.3		59737		2	44.87

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	2.45	2.54	89.7		0.592	3.1	6.3	5411

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	FREE R-VALUE	3P23	2.463	29.182	1.36	59654	3016	96.69	0.2378	0.2354	0.24	0.2829	0.29	rqandom

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	14.045
f_angle_d	0.663
f_chiral_restr	0.038
f_plane_restr	0.005
f_bond_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8931
Nucleic Acid Atoms
Solvent Atoms	80
Heterogen Atoms	90

Software

Software
Software Name	Purpose
PHENIX	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
MOLREP	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.