7NTM | pdb_00007ntm

Cryo-EM structure of S.cerevisiae native alcohol dehydrogenase 1 (ADH1) in its tetrameric apo state


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5ENV 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.569
r_dihedral_angle_4_deg20.792
r_dihedral_angle_3_deg18.792
r_dihedral_angle_1_deg9.091
r_scbond_it8.936
r_long_range_B_refined8.795
r_mcbond_it7.134
r_angle_refined_deg6.76
r_mcangle_it6.571
r_chiral_restr0.582
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.569
r_dihedral_angle_4_deg20.792
r_dihedral_angle_3_deg18.792
r_dihedral_angle_1_deg9.091
r_scbond_it8.936
r_long_range_B_refined8.795
r_mcbond_it7.134
r_angle_refined_deg6.76
r_mcangle_it6.571
r_chiral_restr0.582
r_bond_refined_d0.091
r_gen_planes_refined0.032
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Sample
Tetrameric structure of native ADH1 from S. cereviciae in its apo state.
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles222802
Reported Resolution (Å)2.86
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryD2
Map-Model Fitting and Refinement
Id1 (5ENV)
Refinement SpaceREAL
Refinement ProtocolBACKBONE TRACE
Refinement Target
Overall B Value123
Fitting Procedure
DetailsModel building and refinement were done using using CCP-EM software suite (Burnley et al, 2017). The X-ray structure of yeast ADH1 (PDB: 5ENV) was us ...Model building and refinement were done using using CCP-EM software suite (Burnley et al, 2017). The X-ray structure of yeast ADH1 (PDB: 5ENV) was used as a starting model for model building. This model was docked into our Cryo-EM map using MolRep (Brown et al, 2014). The resulting starting model was manually adjusted in Coot (Emsley et al, 2010). REFMAC 5 (Brown et al, 2014) used for structure model refinement.
Data Acquisition
Detector TypeGATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)60
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)1000
Maximum Defocus (nm)3000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification130000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONWarp40
IMAGE ACQUISITIONEPU2.7
CTF CORRECTIONWarp40
MODEL FITTINGMOLREP
INITIAL EULER ASSIGNMENTcryoSPARCv2.15.041
FINAL EULER ASSIGNMENTcryoSPARCv2.15.041
RECONSTRUCTIONcryoSPARCv2.15.041
MOLECULAR REPLACEMENTMOLREP
MODEL REFINEMENTREFMAC5
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION639189