Please see this post for more background.
The problem is that tick mark labels explicitly specified by code of the form:
text(x(k),y(k),labs{k},'horizontalalignment',horizk,...
'verticalalignment',vertk, ...
'rotation',rotang(k), ...
'fontsize',gfontsize*scl(k), ...
'color',gcolor, ...
'tag','m_grid_xticklabel', ...
'fontname',gfontname);
in Matlab (matlab2tikz is run, .tex compiled with pdflatex) are not properly aligned (vertical only, as far as I can tell) when the 'camera view angle' is adjusted with say, view(45,45).
Here are the axis options from the .tex code:
\begin{axis}[%
width=\figurewidth,
height=\figureheight,
unbounded coords=jump,
clip=false,
view={45}{45},
scale only axis,
xmin=-0.000750572061953379,
xmax=0.000750572061953379,
xtick={-0.0005,0,0.0005},
xticklabels={{-1},{-0.5},{0},{0.5},{1}},
ymin=-0.000901759142452274,
ymax=0.000901887945571112,
ytick={-0.0005,0,0.0005},
yticklabels={{-1},{-0.5},{0},{0.5},{1}},
zmin=-1e+16,
zmax=0,
ztick={-1e+16,-9e+15,-8e+15,-7e+15,-6e+15,-5e+15,-4e+15,-3e+15,-2e+15,-1e+15,0},
hide axis,
axis x line*=bottom,
axis y line*=left,
axis z line*=left,
axis on top,
clip=false
]
as well as, the .tex code associated with the label.
\node[left, inner sep=0mm, rotate=359.980625982625, text=black]
at (axis cs:-0.000768608531802478,0.000872799628421937,0) { 39'};
I have also attached the compiled figure

matlab2tikz. You should post the same question there. A correct solution would probably make use ofxticklabel csandnear xticklabelanchors (and its friends), compare thepgfplotsmanual section "4.9 Axis Descriptions". If you want to repair the figure at hand and you want help here, I suggest to file a complete minimal example such that we can reproduce the figure. – Christian Feuersänger Feb 22 '15 at 18:47matlab2tikzat https://github.com/matlab2tikz/matlab2tikz/issues – Torbjørn T. Feb 22 '15 at 21:22