Reliability of atomic displacement parameters in protein crystal structures

Area of Science:

• Structural Biology
• Crystallography
• Biophysics

Background:

• Atomic displacement parameters (ADPs) quantify atomic motion in protein crystals.
• Accurate estimation of ADP standard errors is crucial for reliable structural comparisons.
• Crystallographic refinement involves restraints that can influence ADP values.

Purpose of the Study:

• To estimate mean standard errors in atomic displacement parameters (ADPs) from protein crystal structure determinations.
• To investigate factors influencing ADP standard errors, including resolution and atomic environment.
• To assess the impact of crystallographic refinement restraints on ADP standard errors.

Main Methods:

• Comparing ADPs of identical protein-chain pairs within the same or different crystals.
• Analyzing ADP standard errors in relation to crystallographic resolution.
• Differentiating ADP standard errors based on atom type (main-chain vs. side-chain) and solvent accessibility.
• Evaluating differences in ADP standard errors for residues in helical versus other secondary structures.

Main Results:

• ADP standard errors increase nearly linearly with decreasing resolution.
• ADP standard errors are greater for side-chain and solvent-exposed atoms compared to main-chain and buried atoms.
• Residues in helical secondary structures exhibit larger ADP standard errors than those in other conformations.
• The study provides insights into the influence of crystallographic refinement restraints on ADP standard errors.

Conclusions:

• The resolution dependence of ADP standard errors is unexpectedly linear.
• Atomic environment and secondary structure significantly impact ADP uncertainty.
• Corrections for refinement restraint influences are recommended when comparing protein structures.