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LH2 complex from Marichromatium purpuratum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LGH
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.0585 f_angle_d 1.293 f_chiral_restr 0.0666 f_bond_d 0.0081 f_plane_restr 0.0075
Sample Light harvesting complex 2 (LH2)
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument HOMEMADE PLUNGER Cryogen Name ETHANE Sample Vitrification Details Blowing time, 10.0 sec.
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 414511 Reported Resolution (Å) 2.38 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C7
Map-Model Fitting and Refinement Id 1 (1LGH, 1LGH) Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target Overall B Value 22.55 Fitting Procedure Details
Data Acquisition Detector Type FEI FALCON IV (4k x 4k) Electron Dose (electrons/Å**2) 43.7
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 800 Maximum Defocus (nm) 2400 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.7 Imaging Mode BRIGHT FIELD Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER Nominal Magnification 120000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cisTEM 1.0 IMAGE ACQUISITION EPU 2.5 CTF CORRECTION CTFFIND 4.1 MODEL FITTING Coot 0.9 MODEL FITTING UCSF Chimera 1.13.1 MODEL REFINEMENT PHENIX 1.17.1 MODEL REFINEMENT REFMAC INITIAL EULER ASSIGNMENT RELION 3.1 FINAL EULER ASSIGNMENT RELION 3.1 CLASSIFICATION RELION 3.1 RECONSTRUCTION RELION 3.1
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 1330154