Experiment: 4YZC

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	The complex of pIRE1a (547-977) with staurosporine was prepared by mixing the protein with 0.5 mM staurosporine and incubated overnight on ice. The crystals were grown at 20C by vapor diffusion in sitting drop containing 2 ul of protein (13 mg/ml in 50 mM Hepes, pH 7.5, 200 mM NaCl, 5 mM DTT, 1 mM EDTA) and 2ul reservoir solution containing PEG 300 (30%-40%), 100 mM Hepes pH 7.5, 200 mM KCl. Small hexagonal plates appeared over 5-10 days and reached full size (0.05 X 0.75 X 0.15 mm) in ~20 days. The crystals were flash-frozen in liquid N2 directly from the crystallization drop. All diffraction data was collected at the Advanced Photon Source, Argonne National Laboratories, Life Sciences CAT, Sector 21

Crystal Properties
Matthews coefficient	Solvent content
3.2	61.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.337	α = 90
b = 155.26	β = 90
c = 155.643	γ = 90

Symmetry
Space Group	P 21 21 21

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	ADSC QUANTUM 315		2012-02-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	0.97872	APS	21-ID-D

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	2.4939	40.23	98.23	0.09722	13.36	6.5		41927			34.12

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	2.4939	2.583	88.06		0.1343		6.2	4710

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3P23	2.494	40.225	1.35	41901	2116	98.17	0.2489	0.2468	0.2892	random

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	12.676
f_angle_d	0.648
f_chiral_restr	0.036
f_plane_restr	0.004
f_bond_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6036
Nucleic Acid Atoms
Solvent Atoms	58
Heterogen Atoms	70

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 R01GM133198.