8X0G | pdb_00008x0g

Human FL Metabotropic glutamate receptor 5, mGlu5-5M with quisqualate, Acc conformation (purified with PAM VU0409551 but not modelled)


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherD_1300042377 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg19.346
r_dihedral_angle_1_deg4.89
r_dihedral_angle_2_deg2.062
r_angle_refined_deg0.94
r_angle_other_deg0.339
r_long_range_B_refined0.225
r_long_range_B_other0.22
r_chiral_restr0.047
r_mcangle_it0.044
r_mcangle_other0.044
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg19.346
r_dihedral_angle_1_deg4.89
r_dihedral_angle_2_deg2.062
r_angle_refined_deg0.94
r_angle_other_deg0.339
r_long_range_B_refined0.225
r_long_range_B_other0.22
r_chiral_restr0.047
r_mcangle_it0.044
r_mcangle_other0.044
r_scangle_other0.031
r_mcbond_it0.023
r_mcbond_other0.023
r_scbond_it0.016
r_scbond_other0.016
r_gen_planes_refined0.004
r_bond_refined_d0.003
r_gen_planes_other0.001
r_bond_other_d
r_dihedral_angle_4_deg
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 FL Metabotropic glutamate receptor 5, mGlu5-5M with quisqualate and PAM VU0409551
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentLEICA EM GP
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles290960
Reported Resolution (Å)3
Resolution MethodFSC 0.143 CUT-OFF
Other DetailsNon-uniform refinement was performed prior to reconstruction
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1
Refinement SpaceRECIPROCAL
Refinement ProtocolOTHER
Refinement Target
Overall B Value100.4
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)49.55
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)1000
Maximum Defocus (nm)2200
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification105000
Calibrated Magnification59523
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging DetailsData was collected in EFTEM with Bioquantum K3
EM Software
TaskSoftware PackageVersion
IMAGE ACQUISITIONEPU
CTF CORRECTIONcryoSPARC
MODEL FITTINGUCSF Chimera1.15
MODEL FITTINGCoot0.9.8.7
RECONSTRUCTIONcryoSPARC
MODEL REFINEMENTPHENIX1.20.1-4487
MODEL REFINEMENTREFMAC5.8.0411
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION3416003