6H7M

ACTIVATED TURKEY BETA1 ADRENOCEPTOR WITH BOUND PARTIAL AGONIST SALBUTAMOL AND NANOBODY Nb6B9


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2H6X2H6X, 3P0G
experimental modelPDB 3P0G2H6X, 3P0G

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52910.1 M Hepes-NaOH pH7.5 and 21-24% PEG1500
Crystal Properties
Matthews coefficientSolvent content
3.8668.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 116.64α = 90
b = 121.5β = 90
c = 130.42γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2016-09-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID30B0.954ESRFID30B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.6125.779959.556733
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.612.68

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 REPLACEMENTTHROUGHOUT2H6X, 3P0G2.7625.7730724159066.760.265710.264730.28515RANDOM82.015
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]
-1.881.480.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.893
r_dihedral_angle_3_deg13.441
r_dihedral_angle_4_deg13.368
r_long_range_B_refined9.279
r_long_range_B_other9.279
r_mcangle_it6.495
r_mcangle_other6.495
r_scangle_other6.041
r_dihedral_angle_1_deg5.561
r_mcbond_it3.895
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.893
r_dihedral_angle_3_deg13.441
r_dihedral_angle_4_deg13.368
r_long_range_B_refined9.279
r_long_range_B_other9.279
r_mcangle_it6.495
r_mcangle_other6.495
r_scangle_other6.041
r_dihedral_angle_1_deg5.561
r_mcbond_it3.895
r_mcbond_other3.895
r_scbond_it3.451
r_scbond_other3.45
r_angle_refined_deg1.299
r_angle_other_deg0.898
r_chiral_restr0.067
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8015
Nucleic Acid Atoms
Solvent Atoms13
Heterogen Atoms203

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing