4RWA

Synchrotron structure of the human delta opioid receptor in complex with a bifunctional peptide (PSI community target)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4N6H	PDB ENTRY 4N6H

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	LIPIDIC CUBIC PHASE	6	293	25-28% (v/v) PEG 400, 0.12 to 0.2 M NaCl, 100 mM MES buffer at pH 6.0, 1 mM DIPP-NH2 and 5% (v/v) of either one of the following additives: 30% glycerol, 1.0 M glycine or 0.01M L-glutathione reduced/0.01M L-glutathione oxidized, Lipidic cubic phase, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.53	65.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 160.549	α = 90
b = 86.121	β = 92.21
c = 94.684	γ = 90

Symmetry
Space Group	C 1 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	100	CCD	MARMOSAIC 300 mm CCD	mirrors	2013-12-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B	1.0330	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	3.28	94.61	96.3	0.173	11.7	4.3		18862

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	3.3	3.51	97.3		0.875	1.9	4.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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 4N6H	3.28	94.61	17904	958	94.68	0.24067	0.23891	0.24	0.27296	0.27	RANDOM	90.825

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]
-3.08		-0.31	1.11		1.98

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.741
r_dihedral_angle_4_deg	18.121
r_dihedral_angle_3_deg	17.824
r_long_range_B_refined	8.432
r_long_range_B_other	8.431
r_mcangle_it	5.36
r_mcangle_other	5.36
r_scangle_other	5.348
r_dihedral_angle_1_deg	5.315
r_mcbond_it	3.296

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5920
Nucleic Acid Atoms
Solvent Atoms	1
Heterogen Atoms	13

Software

Software
Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	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.