5TE5

Crystal structure of Bos taurus opsin regenerated with 6-carbon ring retinal chromophore


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2G87 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2772.8-3.4 M ammonium sulfate in 0.05-0.1 M MES, pH 6.1-6.6, or 0.05-0.1 M NaAcO buffer, pH 5.2-5.6
Crystal Properties
Matthews coefficientSolvent content
4.9475.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.725α = 90
b = 81.725β = 90
c = 200.012γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2016-07-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-C0.97920APS24-ID-C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
14.015099.80.2430.9996.3310.66944

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 REPLACEMENTTHROUGHOUT2G874.0148.53659434899.770.316330.314190.35719RANDOM310.92
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]
5.032.515.03-16.3
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined62.711
r_long_range_B_other62.708
r_mcangle_it46.387
r_mcangle_other46.373
r_scangle_other41.486
r_dihedral_angle_2_deg30.726
r_mcbond_it30.023
r_mcbond_other30.008
r_scbond_it25.681
r_scbond_other25.673
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined62.711
r_long_range_B_other62.708
r_mcangle_it46.387
r_mcangle_other46.373
r_scangle_other41.486
r_dihedral_angle_2_deg30.726
r_mcbond_it30.023
r_mcbond_other30.008
r_scbond_it25.681
r_scbond_other25.673
r_dihedral_angle_3_deg14.712
r_dihedral_angle_4_deg12.463
r_dihedral_angle_1_deg5.642
r_angle_refined_deg1.229
r_angle_other_deg0.952
r_chiral_restr0.065
r_bond_refined_d0.009
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2749
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms21

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing