JHU X-ray Crystallography Facility

"All we have discovered is that it starts with a single individual - always a child - and then spreads explosively, like the formation of crystals round the first nucleus in a saturated solution." Arthur C. Clarke (Childhood's End, 1953)

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Submission

In order to process your request, an application form must be submitted for each individual sample. Our X-ray facility operates on the basis of first-come first-served policy (exceptions can be made for special cases). When you submit your sample(s), please remember it is always best to keep your crystals within the mother liquor/solvent. Doing so might prevent crystal decomposition (especially if the crystal lattice contains some solvent), and allows to pick crystals more readily from the batch (and therefore prevents crystal damage). Herein is the procedure to follow:

1. Download the submission form (a fillable doc or pdf file) - doc | pdf.
2. Fill out the form by providing all necessary information regarding your sample (this is important!).
3. Print, fax (410 516 7044) or email (xray@jhu.edu) the form.

Each sample will be then carefully examined under a stereomicroscope for a preliminary checking. If the sample contains crystals, then a small amount of crystals will be placed on a microscope slide (with some paratone oil) and will be further inspected under cross-polarized light. Most often crystals are found to be single but sometime are found to be twinned. When twin domains are clearly distinguishable (which is often the case), it generally takes little effort to perform microsurgeries on twinned crystals, for which individual domains can be separated (please note this practice might be more difficult with plate-like crystals). Although crystals may appear of good quality (e.g., large crystals, well-defined crystal faces, sharp edges, smooth crystal faces), the last stage of the preliminary examination is to collect a few frames in order to evaluate the diffraction quality. Diffraction patterns of good quality will feature sharp and unsplit reflections at low and high resolution.

Crystals of poor quality

Crystals of good quality

Diffraction pattern of poor quality

Diffraction pattern of good quality

Zip

When X-ray structure determination has been completed, a zip archive file is sent to you via email within 1-2 business days for straightforwad structures or within several days/weeks for difficult structures. A preliminary plot showing the chemical connectivity may be sent to you within the first day of data collection.

An unique reference code is given for each individual structure. The code is referenced as x####n for academic users and as cx####n for non-academic users [x stands for X-ray and cx stand for commercial X-ray; #### is the numbering scheme; n corresponds to the number of attempts done for the same structure and takes the values a (first attempt), b (second attempt), etc.]. Subsequently, the zip file is named either x####n.zip or cx####n.zip.

When the zip file is uncompressed, the structure directory x####n or cx####n is created, and includes 7 subdirectories:

• (c)x####n/bill: this subdirectory contains the issue receipt (pdf file).
  
  
• (c)x####n/cif_final: this subdirectory contains the (c)x####n_final.cif file. This cif file (CIF = Crystallography Information File) includes all necessary information related to the crystal structure and experimental data. This file MUST BE submitted along with your manuscript to the journal of interest. Some journals require to deposit your cif file(s) with the CCDC prior to your manuscript submission. If so, please follow this link for further instructions.
  
  
• (c)x####n/crystal_morphology: this subdirectory contains two digitalized photographs of the crystal that was used for data collection.
  
  
• (c)x####n/experimental_report: this subdirectory contains the experimental.cif and (c)x####n_report.doc files. The experimental.cif file only includes general information about data collection and MUST NOT BE supplied through the process of submitting your manuscript. The .doc file includes the experimental section about X-ray crystallography and the text should be appended either in the manuscript or in the supporting information.
  
  
• (c)x####n/ortep: this subdirectory includes one or several displacement ellipsoid plots (generally drawn at 50% probability level) of the compound of interest. Such plots are typically generated from XP (Shelxtl program), but can also be generated from PLATON or Mercury as well.
  
  
• (c)x####n/platon_report: the subdirectory includes the (c)x####n.chk (cif-file validation) and (c)x####n.ckf (fcf-file validation) files, which are both generated from PLATON. These files are valuable for the crystallographers, but probably not so relevant for the chemists.
  
  
• (c)x####n/refin: the subdirectory includes all necessary files (.res and .hkl) used for the structure refinement.