7EK3 | pdb_00007ek3

Cryo-EM structure of VCCN1 Y332A mutant in lipid nanodisc


ELECTRON MICROSCOPY

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.458
r_dihedral_angle_4_deg20.772
r_lrange_it17.524
r_lrange_other17.509
r_dihedral_angle_3_deg16.271
r_scangle_it13.109
r_scangle_other13.108
r_scbond_it8.768
r_scbond_other8.765
r_mcangle_it8.522
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.458
r_dihedral_angle_4_deg20.772
r_lrange_it17.524
r_lrange_other17.509
r_dihedral_angle_3_deg16.271
r_scangle_it13.109
r_scangle_other13.108
r_scbond_it8.768
r_scbond_other8.765
r_mcangle_it8.522
r_mcangle_other8.515
r_mcbond_it6.157
r_mcbond_other6.148
r_dihedral_angle_1_deg4.991
r_angle_refined_deg1.871
r_angle_other_deg1.711
r_ext_dist_refined_d0.353
r_xyhbond_nbd_refined0.199
r_nbd_refined0.187
r_nbtor_refined0.169
r_nbd_other0.157
r_symmetry_nbd_other0.155
r_symmetry_xyhbond_nbd_refined0.154
r_symmetry_nbd_refined0.106
r_symmetry_nbtor_other0.081
r_chiral_restr0.058
r_symmetry_xyhbond_nbd_other0.023
r_bond_refined_d0.015
r_gen_planes_refined0.005
r_gen_planes_other0.002
r_bond_other_d0.001
Sample
Bestrophin-like protein
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles107192
Reported Resolution (Å)2.7
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC5
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)48
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelTFS KRIOS
Minimum Defocus (nm)
Maximum Defocus (nm)
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
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONRELION3.1
CTF CORRECTIONCTFFIND4.1.13
INITIAL EULER ASSIGNMENTRELION3.1
FINAL EULER ASSIGNMENTRELION3.1
RECONSTRUCTIONRELION3.1
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION