4EJ4

Structure of the delta opioid receptor bound to naltrindole


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4DKLPDB entry 4DKL

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.529329-33% 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 coefficientSolvent content
469.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.278α = 90
b = 73.278β = 90
c = 266.653γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray78CCDMARMOSAIC 300 mm CCDmirrors2012-03-16MSINGLE WAVELENGTH
21x-ray78CCDMARMOSAIC 300 mm CCDmirrors2012-04-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-B1.033APS23-ID-B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
1,23.44098.30.1777.96.512144-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1,23.43.595.80.581.84.3961

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 4DKL3.436.4031.4111916118698.250.25520.25220.2818Random
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]
12.631712.6317-25.2634
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d13.298
f_angle_d1.096
f_chiral_restr0.075
f_bond_d0.006
f_plane_restr0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3351
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms31

Software

Software
Software NamePurpose
Blu-Icedata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling