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 7A5V | pdb_00007a5v

CryoEM structure of a human gamma-aminobutyric acid receptor, the GABA(A)R-beta3 homopentamer, in complex with histamine and megabody Mb25 in lipid nanodisc


ELECTRON MICROSCOPY

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.343
r_dihedral_angle_4_deg17.169
r_long_range_B_refined15.676
r_long_range_B_other15.675
r_dihedral_angle_3_deg13.052
r_scangle_other11.34
r_mcangle_other8.965
r_mcangle_it8.964
r_dihedral_angle_1_deg7.135
r_scbond_it6.905
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.343
r_dihedral_angle_4_deg17.169
r_long_range_B_refined15.676
r_long_range_B_other15.675
r_dihedral_angle_3_deg13.052
r_scangle_other11.34
r_mcangle_other8.965
r_mcangle_it8.964
r_dihedral_angle_1_deg7.135
r_scbond_it6.905
r_scbond_other6.903
r_mcbond_it5.65
r_mcbond_other5.647
r_angle_refined_deg1.3
r_angle_other_deg1.161
r_chiral_restr0.065
r_gen_planes_refined0.018
r_gen_planes_other0.01
r_bond_refined_d0.009
r_bond_other_d
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
Sample
Human GABA(A)R-beta3 homopentamer in complex with Megabody-25 in lipid nanodisc
Sample Components
Human GABA(A)R-beta3 homopentamer
Megabody-25
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentLEICA PLUNGER
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles371693
Reported Resolution (Å)1.7
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC5
Map-Model Fitting and Refinement
Id1
Refinement SpaceRECIPROCAL
Refinement ProtocolAB INITIO MODEL
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeFEI FALCON IV (4k x 4k)
Electron Dose (electrons/Å**2)40
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)300
Maximum Defocus (nm)1100
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification165000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
IMAGE ACQUISITIONEPU
CTF CORRECTIONCTFFIND4.1.13
MODEL FITTINGREFMAC5.8.0270
INITIAL EULER ASSIGNMENTRELION3.1
FINAL EULER ASSIGNMENTRELION3.1
CLASSIFICATIONRELION3.1
RECONSTRUCTIONRELION3.1
MODEL REFINEMENTREFMAC5.8.0270
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION