Cryo-EM structure of the PSII supercomplex from Arabidopsis thaliana
ELECTRON MICROSCOPY
Refinement
RMS Deviations
Key
Refinement Restraint Deviation
f_dihedral_angle_d
11.328
f_angle_d
1.941
f_chiral_restr
0.055
f_plane_restr
0.017
f_bond_d
0.006
Sample
C2S2M2 supercomplex of Photosystem II
Specimen Preparation
Sample Aggregation State
PARTICLE
Vitrification Instrument
FEI VITROBOT MARK III
Cryogen Name
ETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
23434
Reported Resolution (Å)
5.3
Resolution Method
FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type
POINT
Point Symmetry
C2
Map-Model Fitting and Refinement
Id
1
Refinement Space
REAL
Refinement Protocol
FLEXIBLE FIT
Refinement Target
Cross-correlation coefficient
Overall B Value
Fitting Procedure
Details
Initial fitting of the subunits in the cryo-EM map was performed by rigid body real space refinement, using as templates the high resolution crystal ...
Initial fitting of the subunits in the cryo-EM map was performed by rigid body real space refinement, using as templates the high resolution crystal structures of Thermosynechococcus vulcanus PSII (PDB code 3WU2), pea LHC-II (PDB code 2BHW for the S- and M-trimers, and spinach CP29 (PDB code 3PL9) for CP29, CP26 and CP24. Local fitting and adjustment of the subunits in the cryo-EM maps was performed using manual rebuilding and restrained real space
refinement as explained in the primary reference. Due to large differences in local resolution of the cryo-EM map, refinement of the PSII core, the S-trimer with CP26/CP29 and the M-trimer with CP24 was performed separately in excised parts of the cryo-EM map. The core was refined at 4.5 angstrom, the S-trimer+CP26+CP29 at 5.5 angstrom and the M-trimer+CP24 at 6.5 angstrom.
Core: chains A,B,C,D,E,F,H,I,J,K,L,M,O,T,W,X,Z and a,b,c,d,e,f,h,i,j,k,l,m,o,t,w,x,z.
S-trimer+CP26+CP29: chains G,N,Y,S,R and g,n,y,s,r. M-trimer+CP24: chains 1,2,3,4 and 5,6,7,8.
