data for structural papers

This page gives a list of recommended items for inclusion in structural communications in Acta Crystallographica Section D.

Items that are given in a magenta typeface are mandatory.

Click here for more details on these individual items and information on supplying the recommended information in mmCIF format.

If your structure has been solved using NMR, click here for a separate set of recommendations.





1. Sample information

1.1. Macromolecule and source information
Structure name [info]
Component molecules
Additional molecular identifiers
Biological functional unit (BFU) or macromolecular assembly, numbers and types of chains
Mass of BFU (Da)
Macromolecule sequence and chemical configuration [info]
   Sequence database reference code
   Polymers (one-letter code sequence) or Polymer sequence as list of residues
   Ligand, cofactor, ions, solvent
   Mutations
   Post-translational modifications
   Formula weight of entity (Da)
Source organism
   Scientific name
   Strain
   Details
Source gene
   Scientific name
   Strain
   Details
  
1.2 Macromolecule production [info]
For each macromolecular entity
   PCR protocol
   Cloning protocol
   Expression protocol
   Purification protocol
   Additional details
  
1.3. Crystallization [info]
Crystallization method
Temperature (K)
Additional details
Apparatus
Atmosphere
Pressure (kPa)
Crystal growth time
Seeding
Volumes and pHs of crystallization solutions
Compositions of crystallization solutions
Cryo treatments
   Final cryoprotection solution
   Soaking
   Cooling
   Annealing
  
1.4. Crystal data
Space group, crystal system
Unit-cell parameters (Å, °) (s.u. optional)
Crystal dimensions or radius (mm)
Colour of crystal
Crystal habit or shape
No. of molecules in unit cell (Z)
Matthews coefficient VM3 Da-1)
Solvent content (%)


2. Data collection and structure solution statistics
  
2.1. Data collection, refinement data set
Data set identifier
Crystal sample conditions
Diffraction protocol
Sampling protocol
Source of diffracting beam
Focusing and collimation
Monochromator
X-ray beam size
Wavelength (Å)
Detector type
Temperature (K)
Total measuring time (s)
No. of images
Data-processing software
Resolution range and resolution range outer shell (Å)
No. of unique reflections (overall and outer shell)
No. of observed reflections
Criterion for observed reflections
Completeness (%) (overall and outer shell)
Redundancy (overall and outer shell)
< I/σ(I) > (overall and outer shell)
Rmerge (overall and outer shell)
d-spacing (Å) at which < I/σ(I) > = 2 (if this does not occur, leave blank) [info]
  
2.2 Phasing
Phasing method
  
2.2.1. MAD/SAD data and structure solution statistics
MAD/SAD phasing method used
Insertion of MAD/SAD scatterers
Method of locating scatterers
No. of MAD/SAD sets used in phasing
Phasing resolution range (Å)
Phasing power all data; centric, acentric
Figure of merit overall
MAD/SAD solution software
For each phasing set
   Radiation source
   Radiation wavelength
   Temperature (K)
   Resolution range in the phasing data set (Å)
   f' used in phasing
   f'' used in phasing
   Phasing power by set; centric, acentric
   No. of sites
   For each of the sites, the following: site no., atom symbol, occupancy, x, y, z and Biso
  
2.2.2. MIR/MIRAS/SIR/SIRAS data and structure solution statistics
For the MIR application as a whole:
No. of derivatives
Description of the phasing strategy
Resolution range of phasing (Å)
Phasing power all data; acentric, centric
Figure of merit all data
MIR solution software
For each phasing data set (if the native data set used for phasing is not the set used for refinement, it should be described as the first phasing set; additional data sets will correspond to each of the derivatives):
   Radiation source
   Radiation wavelength
   Temperature (K)
   Resolution range of phasing data set (Å)
Then, for each derivative:
   Derivative
   Derivative preparation
   Heavy-atom location method
   Number of sites
   Figure of merit
   For each of the sites, the following: site no., atom symbol, occupancy, x, y, z and Biso
  
2.2.3. Molecular replacement data and structure solution statistics
PDB code for search model
or Identification of search model
If phasing data set is not the data set used for refinement:
   Radiation source
   Radiation wavelength (Å)
   Temperature (K)
   Resolution range (Å)
Molecular replacement phasing details
   Alterations to the search model
   MR solution software


3. Model generation and refinement

Structure refinement software
Refinement on |F|, I, or F2
σ cutoff in data
Resolution range and resolution range outer shell (Å)
No. of reflections used in refinement
No. of reflections above σ cutoff in final cycle
Final overall R factor
Atomic displacement model (iso, aniso, mixed)
Overall average B factor excluding solvent (Å2)
No. of macromolecule atoms refined
No. of ligand atoms
No. of solvent atoms
Total No. of atoms
No. of refined parameters
Non-crystallographic symmetry restraints
Bulk solvent model


4. Model validation

Final Rwork
No. of reflections in test set for Rfree
Final Rfree
Cruickshank DPI
R.m.s. deviations from target values for bond distances, bond angles and
      isotropic B factors (overall, main chain and side chain)
Ramachandran plot analysis
   most favoured regions (%)
   additionally allowed regions (%)
   generously allowed regions (%)
   disallowed regions (%)
Omitted residues