Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Types of Errors: Detection and Minimization01:12

Types of Errors: Detection and Minimization

Error is the deviation of the obtained result from the true, expected value or the estimated central value. Errors are expressed in absolute or relative terms.
Absolute error in a measurement is the numerical difference from the true or central value. Relative error is the ratio between absolute error and the true or central value, expressed as a percentage.
Errors can be classified by source, magnitude, and sign. There are three types of errors: systematic, random, and gross.
Systematic or...
Data Validation01:15

Data Validation

Method validation is a crucial process in analytical chemistry designed to confirm that a given method consistently produces reliable and high-quality results. This process is essential when a method is applied to different sample matrices or when procedural modifications are made, ensuring that the results meet acceptable standards across various applications.
Key parameters for method validation include:
Data Validation01:03

Data Validation

Data validation is an essential part of a comprehensive assessment. Validation is confirming or verifying and opening the door to gathering more assessment data as it clarifies vague or unclear data. The process of checking and verifying the collected information is called data validation. The primary purpose of data validation is to ensure data is as free from error, bias, and misinterpretation as possible.
Nursing assessment guides are generally based on holistic models rather than medical...
Detection of Gross Error: The Q Test01:00

Detection of Gross Error: The Q Test

When one or more data points appear far from the rest of the data, there is a need to determine whether they are outliers and whether they should be eliminated from the data set to ensure an accurate representation of the measured value. In many cases, outliers arise from gross errors (or human errors) and do not accurately reflect the underlying phenomenon. In some cases, however, these apparent outliers reflect true phenomenological differences. In these cases, we can use statistical methods...
Redox Reactions01:24

Redox Reactions

Oxidation-reduction or redox reactions involve the transfer of electrons from one molecule or atom to another. When an atom gains an electron, another atom must lose an electron, meaning oxidation and reduction must occur together. Since the redox occurs in pairs, the atom that gets oxidized is also called the reducing agent or reductant, and the atom that is reduced is also called the oxidizing agent or oxidant. A straightforward way to remember the definitions of oxidation and reduction is...
Redox Reactions01:27

Redox Reactions

Redox reactions are vital biochemical processes that underpin energy metabolism in cells. These reactions involve the transfer of electrons between molecules, occurring in tandem as oxidation and reduction. Oxidation refers to the loss of electrons, while reduction denotes their gain. This coupling ensures the seamless flow of electrons through metabolic pathways. For example, in bacterial metabolism, glucose undergoes oxidation to carbon dioxide, while oxygen is simultaneously reduced to...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Measurement of atomic scattering factors by cryoelectron microscopy.

Proceedings of the National Academy of Sciences of the United States of America·2026
Same author

Insights from aquaporin structures into drug-resistant sleeping sickness.

eLife·2026
Same author

New targets and procedures for validating the valence geometry of nucleic acid structures.

Nucleic acids research·2026
Same author

Halogen bonds between ligands and proteins: Can we use them in validation?

Protein science : a publication of the Protein Society·2025
Same author

Reconstructing biological molecules with help from video gamers.

Acta crystallographica. Section D, Structural biology·2025
Same author

DSSP 4: FAIR annotation of protein secondary structure.

Protein science : a publication of the Protein Society·2025
Same journal

Structural insights into the synthesis of FMN in prokaryotic organisms.

Acta crystallographica. Section D, Biological crystallography·2015
Same journal

Native sulfur/chlorine SAD phasing for serial femtosecond crystallography.

Acta crystallographica. Section D, Biological crystallography·2015
Same journal

Serial crystallographic analysis of protein isomorphous replacement data from a mixture of native and derivative microcrystals.

Acta crystallographica. Section D, Biological crystallography·2015
Same journal

The first crystal structure of the peptidase domain of the U32 peptidase family.

Acta crystallographica. Section D, Biological crystallography·2015
Same journal

Atomic resolution crystal structure of Sapp2p, a secreted aspartic protease from Candida parapsilosis.

Acta crystallographica. Section D, Biological crystallography·2015
Same journal

Structural characterization of a mitochondrial 3-ketoacyl-CoA (T1)-like thiolase from Mycobacterium smegmatis.

Acta crystallographica. Section D, Biological crystallography·2015
See all related articles

Related Experiment Video

Updated: May 23, 2026

RBDT: A Computerized Task System based in Transposition for the Continuous Analysis of Relational Behavior Dynamics in Humans
11:09

RBDT: A Computerized Task System based in Transposition for the Continuous Analysis of Relational Behavior Dynamics in Humans

Published on: July 17, 2021

PDB_REDO: constructive validation, more than just looking for errors.

Robbie P Joosten1, Krista Joosten, Garib N Murshudov

  • 1Department of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands. r.joosten@nki.nl

Acta Crystallographica. Section D, Biological Crystallography
|April 17, 2012
PubMed
Summary
This summary is machine-generated.

The PDB_REDO procedure automatically improves protein data bank (Protein Data Bank) structures using advanced refinement and rebuilding techniques. This process enhances crystallographic and geometric quality, updating static models to current standards.

More Related Videos

Cellular Redox Profiling Using High-content Microscopy
11:37

Cellular Redox Profiling Using High-content Microscopy

Published on: May 14, 2017

Related Experiment Videos

Last Updated: May 23, 2026

RBDT: A Computerized Task System based in Transposition for the Continuous Analysis of Relational Behavior Dynamics in Humans
11:09

RBDT: A Computerized Task System based in Transposition for the Continuous Analysis of Relational Behavior Dynamics in Humans

Published on: July 17, 2021

Cellular Redox Profiling Using High-content Microscopy
11:37

Cellular Redox Profiling Using High-content Microscopy

Published on: May 14, 2017

Area of Science:

  • Structural Biology
  • Biochemistry
  • Computational Biology

Background:

  • The Protein Data Bank (PDB) contains static structural data that may not meet modern crystallographic standards.
  • Improving the quality and accuracy of PDB entries is crucial for downstream research.

Purpose of the Study:

  • To present developments in the PDB_REDO procedure for automated structure improvement.
  • To enhance the quality of macromolecular structures in the PDB.

Main Methods:

  • Utilized a decision-making framework combining re-refinement and rebuilding.
  • Employed software modules for optimal refinement protocol selection (e.g., anisotropic, TLS models) and geometry/data weight optimization.
  • Automated side-chain and peptide plane rebuilding followed by final optimization.

Main Results:

  • Tested on 12,500 PDB entries, demonstrating significant improvements in crystallographic criteria (e.g., R(free)).
  • Showcased enhanced geometric validation criteria across the majority of tested structures.
  • The PDB_REDO database provides improved model statistics and refinement/validation targets.

Conclusions:

  • PDB_REDO effectively updates static PDB structures to contemporary crystallographic standards.
  • The automated procedure requires no expert intervention, making it broadly applicable.
  • The publicly available PDB_REDO database serves as a valuable resource for better refinement and validation.