structural genomics papers

This page gives a list of recommended items for publication in structural genomics papers in  Acta Crystallographica Section D. As many of the items as possible should be included in your paper; items given in grey are optional. The list is provisional; if you have any comments on the list, please send these to lj@iucr.org.
1. Macromolecule details and crystallization
1.1. Macromolecule and source information

Macromolecule name
Macromolecule sequence
Sequence database reference code
Mutations
Post-translational modifications
Macromolecule weight (Da) and estimation method
Biological functional unit, numbers and types of chains
Ligands or cofactors
Source organism name, strain
Source gene, organ, cellular location
Expression system
Host name
Host cell line, strain, variant
Vector, plasmid

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1.2. Crystallization

Crystallization method
Growth temperature (K)
Growth pH
Composition of crystallization solutions

  • Crystallization/precipitant solution
  • Protein solution
  • Drop composition
  • Drop volume
  • Well volume
Additional treatments (e.g. cryoprotectants)
Special conditions (e.g. microgravity, magnetic field, pressure)
Size of crystal used for measurements (mm)
Colour of crystal
Unit-cell parameters (Å, °) (s.u. optional)
Space group, crystal system
No. of molecules in the unit cell (Z)
No. of molecules in the asymmetric unit (Z')
Matthews coefficient VM (Å3 Da-1)
 Solvent content (%)

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2. Data collection and structure solution statistics  
Data for the highest resolution shell should be given in parentheses.

2.1. Data collection

Collection date
Collection site, beamline
Detector type and model
Temperature (K)
Exposure time (s)
Total measuring time (s)
 Number of images
Data-processing software
X-ray beam size

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2.1.1. MAD data and structure solution statistics
Data for each wavelength should be given as appropriate.

Wavelength (Å)
No. of unique reflections
Resolution range (Å)
Completeness (%)
Redundancy
bracket I/sigma Ibracket
Resolution at which bracket I/sigma Ibracket = 2 Å
 Rmerge (%)
Phasing power (acentric, centric)
f '
f ''
Figure of merit
Structure solution software

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2.1.2. MIR data and structure solution statistics
Data for each derivative should be given as appropriate.

Name of derivative
No. of unique reflections
Wavelength (Å)
Resolution range (Å)
Completeness (%)
Redundancy
bracket I/sigma Ibracket
Resolution at which bracket I/sigma Ibracket = 2 Å
Rmerge (%)
Phasing power (acentric, centric)
Figure of merit
Structure solution software

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2.1.3. MR data and structure solution statistics

No. of unique reflections
Wavelength (Å)
Resolution range (Å)
Completeness (%)
Redundancy
bracket I/sigma Ibracket
Resolution at which bracket I/sigma Ibracket = 2 Å
 Rmerge (%)
Structure used as search model
Modifications made to the structure
Resolution range used (Å)
Structure solution software

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2.1.4. MIRAS data and structure solution statistics
Data for each derivative should be given as appropriate.

Name of derivative
No. of unique reflections
Wavelength (Å)
Resolution range (Å)
Completeness (%)
Redundancy
bracket I/sigma Ibracket
Resolution at which bracket I/sigma Ibracket = 2 Å
Rmerge (%)
Phasing power (acentric, centric)
f '
f ''
Figure of merit
Structure solution software

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2.1.5. SIRAS data and structure solution statistics

No. of unique reflections
Wavelength (Å)
Resolution range (Å)
Completeness (%)
Redundancy
bracket I/sigma Ibracket
Resolution at which bracket I/sigma Ibracket = 2 Å
Rmerge (%)
Resolution range used (Å)
Phasing power (acentric, centric)
f '
f ''
Figure of merit
Structure solution software

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2.1.6. SAD data and structure solution statistics

Wavelength (Å)
No. of unique reflections
Resolution range (Å)
Completeness (%)
Redundancy
bracket I/sigma Ibracket
Resolution at which bracket I/sigma Ibracket = 2 Å
Rmerge (%)
Phasing power (acentric, centric)
f '
f ''
Figure of merit
Structure solution software

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3. Structure refinement

Structure refinement software
Refinement type (iso- or anisotropic)
Resolution range (Å)
sigma cutoff in data
No. of reflections used in refinement (working set)
No. of reflections in test set for Rfree
Total no. of reflections if final cycles omitted Rfree check
 Final Rwork (%)
Final Rfree (%)
Final Roverall (%)
 Overall average B factor (Å2)
No. of protein atoms with non-zero occupancy
No. of solvent atoms
No. of other atoms
No. of refined parameters
Coordinate error overall from Cruickshank DPI
R.m.s. deviations

  • Bond distances (Å)
  • Bond angles (°) or distances (Å)

Isotropic B-factor restraints and the computed values

  • Main chain (Å2)
  • Side chain (Å2)

Non-crystallographic symmetry restraints (yes or no)
Bulk solvent B factor
Ramachandran plot analysis

  • Most favored regions (%)
  • Additionally allowed regions (%)
  • Generously allowed regions (%)
  • Disallowed regions (%)

Names of residues omitted from refinement for lack of electron density

  • Complete residues
  • Side chains only
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