8KDF | pdb_00008kdf

Structure of LAT1-CD98hc in complex with JPH203, focused on TMD


ELECTRON MICROSCOPY

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_other58.527
r_long_range_B_refined58.331
r_long_range_B_other58.329
r_mcangle_it40.414
r_mcangle_other40.407
r_scbond_it39.141
r_scbond_other39.132
r_mcbond_it30.051
r_mcbond_other30.051
r_dihedral_angle_2_deg18.611
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_other58.527
r_long_range_B_refined58.331
r_long_range_B_other58.329
r_mcangle_it40.414
r_mcangle_other40.407
r_scbond_it39.141
r_scbond_other39.132
r_mcbond_it30.051
r_mcbond_other30.051
r_dihedral_angle_2_deg18.611
r_dihedral_angle_3_deg14.616
r_dihedral_angle_1_deg6.992
r_angle_refined_deg1.89
r_angle_other_deg0.631
r_chiral_restr0.088
r_bond_refined_d0.01
r_gen_planes_refined0.004
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
LAT1-CD98hc-Fab170
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification Instrument
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles137883
Reported Resolution (Å)3.89
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Map-Model Fitting and Refinement
Id1
Refinement Space
Refinement Protocol
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)51
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelTFS KRIOS
Minimum Defocus (nm)800
Maximum Defocus (nm)2000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging ModeBRIGHT FIELD
Specimen Holder Model
Nominal Magnification
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION