4N6H

1.8 A Structure of the human delta opioid 7TM receptor (PSI Community Target)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4EJ4PDB ENTRY 4EJ4

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1LCP29331-34% (v/v) PEG 400, 0.095 to 0.12 M K/Na tartrate, 5% (v/v) ethylene glycol, 100 mM MES buffer at pH 6.1-6.2, LCP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.7655.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86.23α = 90
b = 72.851β = 107.48
c = 84.408γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDmirrors2013-04-20MSINGLE WAVELENGTH
21CCDMARMOSAIC 300 mm CCDmirrors2013-06-16
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D1.0330APS23-ID-D

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
11.84098.50.10416.44.545488
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)
11.81.8698.50.8222.34.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 4EJ41.829.743157230398.260.172710.171750.19028RANDOM39.313
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]
2.40.03-0.41-1.67
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.636
r_dihedral_angle_4_deg16.747
r_dihedral_angle_3_deg12.935
r_dihedral_angle_1_deg4.852
r_angle_refined_deg1.419
r_angle_other_deg0.851
r_chiral_restr0.085
r_bond_refined_d0.012
r_gen_planes_refined0.007
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.636
r_dihedral_angle_4_deg16.747
r_dihedral_angle_3_deg12.935
r_dihedral_angle_1_deg4.852
r_angle_refined_deg1.419
r_angle_other_deg0.851
r_chiral_restr0.085
r_bond_refined_d0.012
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3089
Nucleic Acid Atoms
Solvent Atoms101
Heterogen Atoms341

Software

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