(1) U115D2dataset.mrcs: this was the particle stack used to reproduce the refinement in RELION
starting from a Gaussian sphere. The dataset was two-fold binned from U115dataset.mrcs.

We made minor modifications to the RELION version 1.1 source code. 
The purpose of these changes was two-fold: 1) to avoid pre-mature progression to finer
angular sampling for images of lower contrast than those tested during the development 
of the original software, and 2) to solve a file resource interlocking issue that 
arises when a greater number of parallel nodes is employed. Three modifications were 
made in the file “ml_optimiser.cpp”, as follows: (i) The function global_mutex.lock() was 
added at line 2220, global_mutex.unlock() at line 2242; (ii) 0.75 was changed to 0.05 at 
line 4684, allowing the finer angular sampling of lower contrast images in autoAdjustAngularSampling(); 
and (iii) Line 4656 was changed to “max_nr_iter_wo_resol_gain = (do_split_random_halves) ? 0 : 6” 
in autoAdjustAngularSampling(). These changes are not essential for successful refinement 
when one follows the author’s suggestion of starting from a 60-Å low-pass filtered model. 
However, we found the changes to be critical for successful refinement when a Gaussian sphere 
was used as a starting model.

(2) U115dataset.mrcs: this is the particle set with the original pixel size. It is a subset of the
larger dataset deposited as the *.dat SPIDER stack files.

(3) All raw particle images in the *.dat SPIDER stack files were only inverted in contrast without 
any further processing such as filtering or binning.

(4) Defocus information is provided in the *.star and sel_group.dat files.