Data Processing Programs for Analysis of Diffraction Images of Macromolecular Crystals Recorded using Synchrotron Radiation

Abstract

Besides the crystal preparation, the rst and crucial step in the process of protein structure determination is proper processing of the collected diraction images, as they provide the experimental observations used throughout the entire process of structure solution and renement. In the last two decades several computer programs have been developed. Among the most used and popular are: HKL2000, MOSFLM, d*TREK and XDS package. To nd out the advantages and disadvantages of the data processing programs, several very dierent data sets, including diraction data from DNA/RNA and protein crystals were tested. It has been found that all the major programs for processing and analysis of diraction data give excellent and comparable results with good quality, medium resolution data sets, but their treatment of very high resolution or imperfect data diers in terms of indexing, spot integration, scaling and the treatment of errors. If the diraction data are of good quality and the problem is relatively straightforward, the automated approach to data processing may be most appropriate. On the other hand, if one is trying to squeeze out as much information from the experimental data as possible, then only expert manual processing can be successful, regardless of the data quality.

Structure-Based Design of 4-Hydroxyphenylpyruvate Dioxygenase Inhibitor as a Potential Herbicide for Cotton Fields

“…The HKL2000 package was used to handle the collected reflections by reducing, merging, and scaling. 39 In addition, by defining the cocrystal structure of AtHPPD-methylbenquitrione (PDB ID: 5YWK) as the standard model, the Collaborative Computational Project 4 Program Phaser was utilized to execute the molecular replacement. Then, we adjusted the standard model using PHENIX and Coot.…”

“…The diffraction data of At HPPD- 23 were gathered by an X-ray beam at the 19 U1 beamline located in the Shanghai Synchrotron Radiation Facility. The HKL2000 package was used to handle the collected reflections by reducing, merging, and scaling . In addition, by defining the co-crystal structure of At HPPD-methylbenquitrione (PDB ID: 5YWK) as the standard model, the Collaborative Computational Project 4 Program Phaser was utilized to execute the molecular replacement.…”

Modulation of biliverdin dynamics and spectral properties by Sandercyanin

“…The images were indexed, integrated, and scaled using HKL2000 (ref. 18 )/d*TREK 19 /MOSFLM. 20 Structures were determined by molecular replacement method using Phaser 21 and the wild-type SFP structure (PDB ID: ) as starting model.…”

In Situ Proteolysis Condition-Induced Crystallization of the XcpVWX Complex in Different Lattices

“…Complete data sets containing 360 frames of images were collected at a 1.033-Å wavelength at 100 K from a single crystal with the exposure of 1 s per frame. As XDS is a fast and efficient software package for processing twinned data, it was used to index and scale our datasets [53]. The structure of the XcpVWX complex was phased by molecular replacement (Phaser) using the high-quality crystal structure of the XcpVWX complex (PDB ID:5VTM) as a search model.…”