Experiment: 4DKL

Crystal structure of the mu-opioid receptor bound to a morphinan antagonist

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	LIPIDIC CUBIC PHASE	7	293	100 mM HEPES, pH 7.0, 300 mM lithium sulfate, 7.5% DMSO, 30-38% PEG400 in monoolein:cholesterol mixed in a 10:1 ratio, LIPIDIC CUBIC PHASE, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.82	67.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.882	α = 90
b = 174.73	β = 107.84
c = 68.353	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	78	CCD	MARMOSAIC 300 mm CCD	Mirrors	2011-11-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	1.033	APS	23-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	2.8	30.5	99	0.144	10.6	5.8		19145		-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	2.8	2.9	99.3		0.788	1.8	5.5	1907

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 3ODU	2.8	30.488	1.37	18974	946	97.54	0.2347	0.2326	0.2324	0.2753	0.2699	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]
23.1886		9.0174	-18.4026		-4.786

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	12.615
f_angle_d	0.928
f_chiral_restr	0.057
f_bond_d	0.005
f_plane_restr	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3476
Nucleic Acid Atoms
Solvent Atoms	37
Heterogen Atoms	177

Software

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