Synthetic single particle cryo-EM dataset of the SARS-CoV-2 spike protein

PDBs were generated using molecular dynamics. See DESRES_README.txt for more details on molecular dynamics simulation. PDBs were converted to volumetric data using EMAN2. The image stack contains 100 000 projection images each  of the 10 states (see PDBs), at an SNR of 1/10 in the following order: state00 (closed) state01 (closed) state02 (closed) state10 (intermediate) state11 (intermediate) state12 (intermediate) state13 (intermediate) state20 (open) state21 (open) state22 (open) Projections were made using relion_project.    White gaussian noise with standard deviation 1.0   CTF multiplied signal   High signal-to-noise ratio   Image size 96x96x96    MRC-files used for the projections not included, but can be generated using the PDB files. Final RELION reconstruction resolution is 5.33334 Angstrom (Nyqvist is at 5.33334). Command line for RELION reconstruction: relion_refine_mpi --o refine3d/run --auto_refine --split_random_halves --i rot_trans_ctf_noise/stack.star --ref pdb2mrc/state21.mrc --ini_high 20 --dont_combine_weights_via_disc --preread_images --pool 30 --pad 2 --ctf --particle_diameter 130 --flatten_solvent --zero_mask --oversampling 1 --healpix_order 2 --auto_local_healpix_order 4 --offset_range 5 --offset_step 2 --low_resol_join_halves 40 --norm --scale --j 2 --gpu --fristiter_cc --grad  This dataset is generated as a testbed for cryo-EM heterogeneity analysis.