pdb_extract - Tutorial

Tutorial for processing a structure solved by X-ray crystallography

The pdb_extract online tool extracts essential details from each step of your structure determination process in preparation for PDB deposition. Refinement statistics, for the most part, will be extracted from the header of your coordinate file. However, if it does not list specific statistics, the LOG files you provide within pdb_extract should supply these extra values. Such information is essential to include in today's PDB entries.

By providing the necessary files and information, you will receive two files in return: one mmCIF file with coordinate and refinement statistics (pdb_extract_coord_#.cif), and the other contains your structure factors (pdb_extract_sf_#.cif). The two files can be used as input for Validation and deposition to ADIT or ADITBeta.

Step 1: Make sure that the X-ray option is selected at pdb-extract.rcsb.org/.

Step 2: Upload your fully refined coordinate file into the box provided.

Step 3: Select the file format (PDB or mmCIF) and program used to refine the coordinates.

Step 4: Click the run button to start pdb_extract.

The next series of forms will capture each essential step of the structure determination method,
including all structure factors and resulting output/LOG files used for structure refinement and
protein phasing. Items marked with an asterisk (*) are required.

Form 1: Information about Authors, Detectors...
You can either upload the file that you have filled out offline (available here), or you can complete it online
during the pdb_extract process by following the "click here to complete this entry on line" link.

Guidelines and examples for filling out the author information file are listed at the top of the file.

Form 2: Convert Structure Factors to mmCIF format

• Upload the structure factors file used for final cycle of refinement.
• Select the data format and type (or program names) used for its refinement.
• Upload the reflection files required for protein phase determination, and provide their data format
  and type (or program names) as well. Experiments that used molecular replacement for phasing can skip this step.

Form 3: Extract Statistical Information from Steps of Structure Determination
This frame is used to extract key detail information from structure determination steps: protein phasing,
molecular replacement, density modification, and final structure refinement.



• Upload the output file names exported from each crystallographic application step.
• Select the program names and file formats as required.

Final form: Confirmation of crystallographic parameters and macromolecular sequence

• Modify the chemical sequence in the molecular entity group to match the full protein sequence used in this experiment.
  Missing residues that appear as question marks "?" must be replaced with their actual amino acid composition.
• Confirm that the correct molecular entity chains exist.
• Confirm that the polymer type is correct.
• If this structure is a result of a structural genomics project, enter the Target ID here as well.

Step 5: Begin the extraction!

• Click the RUN button in the bottom of the lower frame.
• Processing takes approximately 5 minutes, perhaps longer if your files are very large.
• Save the mmCIF files (pdb_extract_coord_#.cif and pdb_extract_sf_#.cif) onto your local computer.

NEXT: Upload these two mmCIF files to ADIT or ADITBeta for data submission.

Note: if you need help for each entry, click the corresponding help button for the entry.

Questions, comments, and suggestions should be sent to deposit@deposit.rcsb.org.