6H7O

ACTIVATED TURKEY BETA1 ADRENOCEPTOR WITH BOUND WEAK PARTIAL AGONIST CYANOPINDOLOL 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
3.867.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 116.573α = 90
b = 119.963β = 90
c = 130.096γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 4M2015-11-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE MASSIF-30.968ESRFMASSIF-3

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
12.7938.2298.33.79.845172
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.792.89

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,3P0G2.838.2222672112452.050.24170.24010.27371RANDOM80.741
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]
-0.990.370.62
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.948
r_dihedral_angle_4_deg13.952
r_dihedral_angle_3_deg12.44
r_long_range_B_refined8.808
r_long_range_B_other8.795
r_mcangle_it5.935
r_mcangle_other5.935
r_dihedral_angle_1_deg5.131
r_scangle_other4.97
r_mcbond_it3.447
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.948
r_dihedral_angle_4_deg13.952
r_dihedral_angle_3_deg12.44
r_long_range_B_refined8.808
r_long_range_B_other8.795
r_mcangle_it5.935
r_mcangle_other5.935
r_dihedral_angle_1_deg5.131
r_scangle_other4.97
r_mcbond_it3.447
r_mcbond_other3.447
r_scbond_it2.735
r_scbond_other2.735
r_angle_refined_deg1.244
r_angle_other_deg0.87
r_chiral_restr0.06
r_bond_refined_d0.008
r_gen_planes_refined0.004
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7977
Nucleic Acid Atoms
Solvent Atoms7
Heterogen Atoms206

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing