9DYL | pdb_00009dyl

BEST1 + PABA open state


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 8D1I 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.565
r_dihedral_angle_4_deg17.258
r_long_range_B_refined16.327
r_long_range_B_other16.327
r_dihedral_angle_3_deg13.865
r_scangle_other11.661
r_mcangle_it8.249
r_mcangle_other8.249
r_scbond_it7.231
r_scbond_other7.231
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.565
r_dihedral_angle_4_deg17.258
r_long_range_B_refined16.327
r_long_range_B_other16.327
r_dihedral_angle_3_deg13.865
r_scangle_other11.661
r_mcangle_it8.249
r_mcangle_other8.249
r_scbond_it7.231
r_scbond_other7.231
r_mcbond_it5.616
r_mcbond_other5.614
r_dihedral_angle_1_deg5.229
r_angle_other_deg1.58
r_angle_refined_deg1.343
r_chiral_restr0.074
r_bond_refined_d0.011
r_gen_planes_refined0.007
r_gen_planes_other0.003
r_bond_other_d0.001
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
BEST1 + PABA open state
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles41771
Reported Resolution (Å)2.6
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1 (8D1I)
Refinement Space
Refinement ProtocolRIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)58
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelTFS KRIOS
Minimum Defocus (nm)800
Maximum Defocus (nm)1500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder Model
Nominal Magnification105000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:
IMAGE ACQUISITIONLeginon
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION488010