6ZJA

Helicobacter pylori urease with inhibitor bound in the active site


ELECTRON MICROSCOPY

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d18.089
f_angle_d0.854
f_chiral_restr0.057
f_plane_restr0.006
f_bond_d0.005
Sample
1.1 MDa Helicobacter pylori Urease
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles187461
Reported Resolution (Å)2
Resolution MethodFSC 0.5 CUT-OFF
Other DetailsRelion was used for resconstruction
Refinement Type
Symmetry TypePOINT
Point SymmetryT
Map-Model Fitting and Refinement
Id1 (1E9Z, 1E9Z)
Refinement SpaceREAL
Refinement ProtocolRIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)50
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 CS
Imaging ModeBRIGHT FIELD
Specimen Holder Model
Nominal Magnification
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
CTF CORRECTIONRELION3.0 beta
MODEL FITTINGCoot0.8.9
INITIAL EULER ASSIGNMENTRELION3.0 beta
FINAL EULER ASSIGNMENTRELION3.0 beta
CLASSIFICATIONRELION3.0 beta
RECONSTRUCTIONRELION3.0 beta
MODEL REFINEMENTPHENIX1.18
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
NONERelion 3.0 beta per image and per particle203000