9GE4 | pdb_00009ge4

CryoEM structure of the human INO80 core- H2A.Z nucleosome complex


ELECTRON MICROSCOPY

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined50.065
r_long_range_B_other50.065
r_scangle_other37.916
r_mcangle_it26.315
r_mcangle_other26.312
r_scbond_it23.468
r_scbond_other23.467
r_mcbond_it16.841
r_mcbond_other16.841
r_dihedral_angle_3_deg14.5
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined50.065
r_long_range_B_other50.065
r_scangle_other37.916
r_mcangle_it26.315
r_mcangle_other26.312
r_scbond_it23.468
r_scbond_other23.467
r_mcbond_it16.841
r_mcbond_other16.841
r_dihedral_angle_3_deg14.5
r_dihedral_angle_1_deg8.51
r_dihedral_angle_2_deg8.407
r_angle_refined_deg1.975
r_angle_other_deg0.664
r_chiral_restr0.092
r_gen_planes_refined0.016
r_bond_refined_d0.009
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 INO80 remodeller with H2A.Z containing nucleosomes
Sample Components
Histone Octamer
Synthetic deoxyribonucleic acid
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentLEICA EM GP
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles94892
Reported Resolution (Å)3.52
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1
Refinement SpaceRECIPROCAL
Refinement ProtocolFLEXIBLE FIT
Refinement TargetMAXIMUM LIKELIHOOD WITH PHASES
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)1
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)1100
Maximum Defocus (nm)2900
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder Model
Nominal Magnification
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONcryoSPARC4.5.3
CTF CORRECTIONcryoSPARC4.5.3
MODEL FITTINGCoot0.9.8.93
MODEL FITTINGISOLDE1.8
INITIAL EULER ASSIGNMENTcryoSPARC4.5.3
FINAL EULER ASSIGNMENTcryoSPARC4.5.3
MODEL REFINEMENTREFMAC5.8.0425
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION12419217Minimum particle diameter (A) = 120 Maximum particle diameter (A) = 240