5O8F

Structure of a chimaeric beta3-alpha5 GABAA receptor in complex with nanobody Nb25 and pregnanolone


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4COF 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.627714% PEG 6000, 0.1M N-(2-Acetamido)iminodiacetic acid (ADA), 7.6 mM 4-Cyclohexyl-1-Butyl-beta-D-Maltoside (CYMAL-4)
Crystal Properties
Matthews coefficientSolvent content
3.564.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 290.102α = 90
b = 290.102β = 90
c = 290.102γ = 90
Symmetry
Space GroupI 2 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2015-07-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9763DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
13.1949.7521000.6210.1310.9866.830.46692868.2
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.193.311003.1310.6090.2151.225.5

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 REPLACEMENTTHROUGHOUT4COF3.2205.1363621330499.960.232960.232460.2424RANDOM70.752
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.33
r_dihedral_angle_3_deg12.369
r_dihedral_angle_4_deg11.664
r_dihedral_angle_1_deg5.452
r_long_range_B_refined5.237
r_long_range_B_other5.237
r_scangle_other2.002
r_mcangle_it1.915
r_mcangle_other1.915
r_scbond_it1.164
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.33
r_dihedral_angle_3_deg12.369
r_dihedral_angle_4_deg11.664
r_dihedral_angle_1_deg5.452
r_long_range_B_refined5.237
r_long_range_B_other5.237
r_scangle_other2.002
r_mcangle_it1.915
r_mcangle_other1.915
r_scbond_it1.164
r_scbond_other1.164
r_angle_refined_deg1.121
r_mcbond_it1.095
r_mcbond_other1.095
r_angle_other_deg0.895
r_chiral_restr0.061
r_bond_refined_d0.007
r_gen_planes_refined0.005
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 Atoms18217
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms600

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building