6B20

Crystal structure of a complex between G protein beta gamma dimer and an inhibitory Nanobody regulator


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1A0R 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION277.1525-30% (w/v) PEG 3350 in 0.1-0.2 M Bis-Tris-HCl, pH 5.5-5.7, and 0.2-0.3 M MgCl2
Crystal Properties
Matthews coefficientSolvent content
2.3848.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.66α = 90
b = 77.23β = 109.8
c = 101.66γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100.15PIXELDECTRIS EIGER X 16M2017-07-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-E0.97918APS24-ID-E

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rpim I (All)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
12.3447.8299.60.220.9916.284.3142434
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.342.499.81.770.5071.054.43

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 REPLACEMENTTHROUGHOUT1A0R2.3447.8242434223499.650.202830.200340.24906RANDOM52.181
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]
0.11-1.953.38-1.66
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.312
r_dihedral_angle_4_deg17.718
r_dihedral_angle_3_deg14.897
r_long_range_B_refined9.97
r_long_range_B_other9.966
r_dihedral_angle_1_deg7.107
r_scangle_other6.105
r_mcangle_it5.635
r_mcangle_other5.634
r_scbond_it3.869
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.312
r_dihedral_angle_4_deg17.718
r_dihedral_angle_3_deg14.897
r_long_range_B_refined9.97
r_long_range_B_other9.966
r_dihedral_angle_1_deg7.107
r_scangle_other6.105
r_mcangle_it5.635
r_mcangle_other5.634
r_scbond_it3.869
r_scbond_other3.869
r_mcbond_it3.637
r_mcbond_other3.635
r_angle_refined_deg1.574
r_angle_other_deg0.988
r_chiral_restr0.092
r_bond_refined_d0.012
r_gen_planes_refined0.006
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 Atoms7872
Nucleic Acid Atoms
Solvent Atoms396
Heterogen Atoms12

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing