5DQQ

Structure, inhibition and regulation of two-pore channel TPC1 from Arabidopsis thaliana

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	9.3	293	0.1 M glycine, pH 9.3, 50 mM potassium chloride, 1 mM calcium chloride, 35% PEG300

Crystal Properties
Matthews coefficient	Solvent content
4.41	72.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.18	α = 90
b = 154.81	β = 90
c = 219.77	γ = 90

Symmetry
Space Group	C 2 2 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 315r		2015-02-24	M	SINGLE WAVELENGTH
2	1	x-ray		CCD	ADSC QUANTUM 315r			M	SINGLE WAVELENGTH
3	1	x-ray		PIXEL	DECTRIS PILATUS 6M			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	1, 1.006, 1.25465, 1.3854, 1.75	ALS	8.3.1
2	SYNCHROTRON	ALS BEAMLINE 5.0.2		ALS	5.0.2
3	SYNCHROTRON	SSRL BEAMLINE BL12-2		SSRL	BL12-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	2.7	109.885	93.9	0.156	0.156	10.42	7.3	36476	21275			108

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.7	3	81.4		0.732	7.328	0.31	7.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	Mean Isotropic B
X-RAY DIFFRACTION	MIRAS	THROUGHOUT	2.872	38.703	1.33	21270	1052	61.27	0.299	0.297	0.3394	110.3123

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	17.699
f_angle_d	0.744
f_chiral_restr	0.04
f_bond_d	0.004
f_plane_restr	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5282
Nucleic Acid Atoms
Solvent Atoms	57
Heterogen Atoms	63

Software

Software
Software Name	Purpose
PHENIX	refinement
SHARP	phasing
DM	phasing
XDS	data reduction
XSCALE	data scaling

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.