5GJQ | pdb_00005gjq

Structure of the human 26S proteasome bound to USP14-UbAl


ELECTRON MICROSCOPY

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined60.556
r_long_range_B_other60.556
r_scangle_other40.995
r_mcangle_it36.721
r_mcangle_other36.72
r_dihedral_angle_2_deg35.643
r_scbond_it24.773
r_scbond_other24.773
r_mcbond_it22.714
r_mcbond_other22.714
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined60.556
r_long_range_B_other60.556
r_scangle_other40.995
r_mcangle_it36.721
r_mcangle_other36.72
r_dihedral_angle_2_deg35.643
r_scbond_it24.773
r_scbond_other24.773
r_mcbond_it22.714
r_mcbond_other22.714
r_dihedral_angle_4_deg19.056
r_dihedral_angle_3_deg18.733
r_dihedral_angle_1_deg8.845
r_angle_refined_deg1.768
r_angle_other_deg0.973
r_chiral_restr0.091
r_bond_refined_d0.016
r_gen_planes_refined0.008
r_bond_other_d0.003
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
Sample
human 26S proteasome bound to USP14-UbAl
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Detailsblot for 2 seconds before plunging
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles141293
Reported Resolution (Å)4.35
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 TypeFEI FALCON II (4k x 4k)
Electron Dose (electrons/Å**2)37
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)
Maximum Defocus (nm)
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging DetailsPreliminary grid screening was performed manually
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONRELION1.4
IMAGE ACQUISITIONEPU
CTF CORRECTIONCTFFIND3
MODEL FITTINGChimera1.10.1
MODEL REFINEMENTREFMAC4.5
INITIAL EULER ASSIGNMENTRELION1.4
FINAL EULER ASSIGNMENTRELION1.4
CLASSIFICATIONRELION1.4
RECONSTRUCTIONRELION1.4
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION534096