Please check the shape of the nanoparticles, if the faceted shapes are different, then the nanoparticles may have prefered growth direction so that the intensity of reflections in XRD patterns are different.

Normally  for the crystalline  nano-particle state,  Au XRD spectrum should and does show  (111),( 200), (220) and  (311) peaks  in the range of  [2theta = 35o  - 80o] superimposed on the background, which may include (002) graphite peak trace. Where (111)  peak  appears to be extremely sharp and intense.

I do see any logical reason to explain why you have got very strange results in terms of defected crystallization or quasi-amorphous behavior using X-diffraction theory in  highly imperfect solid particles which are lacking scattering coherency.  

Please post your XRD data with all the juicy details about sample, sample prep (processing history) and optics used for the best feed-back!

 Dear Michael Kitching,

I do not have any experience on producing Au nanoparticlles via the biotechnological protein way. In case your specimen can be conceived as a random powder specimen, the presence of Au311-peak seems to be quite usual. The relative integrated intensity of this peak for a random powder specimen can be established using the standard procedures as described by the common textbooks on XRD. In a zero approach I would suggest that deviations from the ad random integrated intensity would evoke from preferred orientations or textures. So, a possible explanation might be found by studying the nanoparticles obtained from the other protein extracts. 

Dear Michael Kitching,

To say the truth, nanoparticles are not good for XRD measurements.  Nanomaterials are frequently X-Ray amorphous because the minimal XRD coherent scattering region in XRD is usually not less than about 5 nm.  To study nanopowders it is better to use short wave length irradiation like Mo. 

See, for instance, the reference:

Nanostructure by high-energy X-ray diffraction

Materials Today

Volume 11, Issue 11, Pages 28–38Valeri Petkov

You difference in XRD patterns signifies the different conditions of crystal growth and preferred direction of the latter.

Conference Paper High-Energy x-Ray Diffraction Study of Nano-Scale Materials

 Dear Michael Kitching,

Some remarks:

1. Au111, Au220 reflections present for Au-nano particles from three protein extracts.

2. Au311 reflection only present for Au-nano particles from one protein extract.

3. Source of X-rays is not given; presumably CuKalfa?

4. Decreasing the coherent scattering region may help in fulfilling the random powder condition (by selecting a Mo radiation). However, assuming that the nanoparticle size is more or less the same for the three protein extracts, it seems that this is not the real problem, as for the third protein extract sufficient reflections were present. 

5. So, a possible explanation might be found by studying the nanoparticles obtained from the protein extracts without the Au311 reflection. 

6. Textures and/or particle size line broadening are suggested to be incorporated in an explanation.