Experiment: 4EJ4

Structure of the delta opioid receptor bound to naltrindole

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5	293	29-33% PEG 400, 100 mM HEPES pH 7.5, 120-180 mM sodium citrate, 350 mM Magnesium chloride. Protein was mixed 1:1.5 (w:w) with 91% monoolein 9% cholesterol mixture by weight, Lipidic cubic phase, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
4	69.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.278	α = 90
b = 73.278	β = 90
c = 266.653	γ = 120

Symmetry
Space Group	P 31 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	78	CCD	MARMOSAIC 300 mm CCD	mirrors	2012-03-16	M	SINGLE WAVELENGTH
2	1	x-ray	78	CCD	MARMOSAIC 300 mm CCD	mirrors	2012-04-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B	1.033	APS	23-ID-B

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	3.4	40	98.3	0.177	7.9	6.5		12144		-3

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	3.4	3.5	95.8		0.58	1.8	4.3	961

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	THROUGHOUT	PDB entry 4DKL	3.4	36.403	1.41	11916	1186	98.25	0.2552	0.2522	0.2557	0.2818	0.2853	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]
12.6317			12.6317		-25.2634

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	13.298
f_angle_d	1.096
f_chiral_restr	0.075
f_bond_d	0.006
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3351
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	31

Software

Software
Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling