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Helicobacter pylori urease with inhibitor bound in the active site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1E9Z
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 18.089 f_angle_d 0.854 f_chiral_restr 0.057 f_plane_restr 0.006 f_bond_d 0.005
Sample 1.1 MDa Helicobacter pylori Urease
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 187461 Reported Resolution (Å) 2 Resolution Method FSC 0.5 CUT-OFF Other Details Relion was used for resconstruction Refinement Type Symmetry Type POINT Point Symmetry T
Map-Model Fitting and Refinement Id 1 (1E9Z, 1E9Z) Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K2 SUMMIT (4k x 4k) Electron Dose (electrons/Å**2) 50
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) Maximum Defocus (nm) Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS Imaging Mode BRIGHT FIELD Specimen Holder Model Nominal Magnification Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version CTF CORRECTION RELION 3.0 beta MODEL FITTING Coot 0.8.9 INITIAL EULER ASSIGNMENT RELION 3.0 beta FINAL EULER ASSIGNMENT RELION 3.0 beta CLASSIFICATION RELION 3.0 beta RECONSTRUCTION RELION 3.0 beta MODEL REFINEMENT PHENIX 1.18
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details NONE Relion 3.0 beta per image and per particle 203000