4PXF

Crystal structure of the active G-protein-coupled receptor opsin in complex with the finger-loop peptide derived from the full-length arrestin-1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3DQB 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP62773.2 M (NH4)2SO4 in 0.1 M 2-(N-morpholino)ethanesulfonic acid (MES), pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 242.622α = 90
b = 242.622β = 90
c = 110.216γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-Fmirrors2012-07-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.9791ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.7540.0499.60.050.0523.17.4321663216670.4
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)
12.752.999.20.94427.34645

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3DQB2.7540.043051130511163799.660.216590.216590.214760.25075RANDOM84.895
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]
-1.17-1.17-1.173.79
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_bonded42.816
r_sphericity_free40.117
r_dihedral_angle_2_deg36.438
r_scangle_other19.421
r_long_range_B_refined19.062
r_long_range_B_other19.038
r_scbond_it16.421
r_scbond_other16.412
r_mcangle_it16.286
r_mcangle_other16.284
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_bonded42.816
r_sphericity_free40.117
r_dihedral_angle_2_deg36.438
r_scangle_other19.421
r_long_range_B_refined19.062
r_long_range_B_other19.038
r_scbond_it16.421
r_scbond_other16.412
r_mcangle_it16.286
r_mcangle_other16.284
r_dihedral_angle_3_deg15.713
r_mcbond_it13.846
r_mcbond_other13.834
r_dihedral_angle_4_deg12.246
r_rigid_bond_restr6.208
r_dihedral_angle_1_deg5.104
r_angle_refined_deg1.187
r_angle_other_deg0.798
r_chiral_restr0.154
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2635
Nucleic Acid Atoms
Solvent Atoms11
Heterogen Atoms159

Software

Software
Software NamePurpose
MxCuBEdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling