Global indicators of X-ray data quality

2001 ◽  
Vol 34 (2) ◽  
pp. 130-135 ◽  
Author(s):  
Manfred S. Weiss
Keyword(s):  
Data Quality ◽  
Diffraction Data ◽  
Optical Resolution ◽  
Data Set ◽  
X Ray ◽  
Global Indicators ◽  
Nominal Resolution

Global indicators of the quality of diffraction data are presented and discussed, and are evaluated in terms of their performance with respect to various tasks. Based on the results obtained, it is suggested that some of the conventional indicators still in use in the crystallographic community should be abandoned, such as the nominal resolutiondminor the mergingRfactorRmerge, and replaced by more objective and more meaningful numbers, such as the effective optical resolutiondeff,optand the redundancy-independent mergingRfactorRr.i.m.. Furthermore, it is recommended that the precision-indicating mergingRfactorRp.i.m.should be reported with every diffraction data set published, because it describes the precision of the averaged measurements, which are the quantities normally used in crystallography as observables.

scholarly journals Identification of the point of diminishing returns in high-multiplicity data collection for sulfur SAD phasing

2017 ◽  
Vol 24 (1) ◽  
pp. 19-28 ◽  
Author(s):  
Selina L. S. Storm ◽  
Fabio Dall'Antonia ◽  
Gleb Bourenkov ◽  
Thomas R. Schneider
Keyword(s):  
Data Collection ◽  
Data Quality ◽  
Radiation Damage ◽  
Diffraction Data ◽  
High Multiplicity ◽  
X Ray ◽  
Anomalous Data ◽  
Diminishing Returns ◽  
Sad Phasing

High-quality high-multiplicity X-ray diffraction data were collected on five different crystals of thaumatin using a homogeneous-profile X-ray beam at E = 8 keV to investigate the counteracting effects of increased multiplicity and increased radiation damage on the quality of anomalous diffraction data collected on macromolecular crystals. By comparing sulfur substructures obtained from subsets of the data selected as a function of absorbed X-ray dose with sulfur positions in the respective refined reference structures, the doses at which the highest quality of anomalous differences could be obtained were identified for the five crystals. A statistic σ{ΔF} D , calculated as the width σ of the normalized distribution of a set {ΔF} of anomalous differences collected at a dose D, is suggested as a measure of anomalous data quality as a function of dose. An empirical rule is proposed to identify the dose at which the gains in data quality due to increased multiplicity are outbalanced by the losses due to decreases in signal-to-noise as a consequence of radiation damage. Identifying this point of diminishing returns allows the optimization of the choice of data collection parameters and the selection of data to be used in subsequent crystal structure determination steps.

Fine-needle capillary mounting for protein microcrystals

2012 ◽  
Vol 45 (4) ◽  
pp. 785-788 ◽  
Author(s):  
Masatomo Makino ◽  
Izumi Wada ◽  
Nobuhiro Mizuno ◽  
Kunio Hirata ◽  
Nobutaka Shimizu ◽  
...  
Keyword(s):  
Data Quality ◽  
Optical Tweezers ◽  
Diffraction Data ◽  
Cell Biology ◽  
Capillary Action ◽  
Fine Needle ◽  
X Ray

Protein microcrystals of less than 10 µm in size are now applicable to X-ray studies by synchrotron microbeam technology. However, because of their small size, they are difficult to handle and mount. In addition, the deterioration of data quality by scattering from the mounting apparatus and crystallization solvent is not negligible. To address these issues, a simple mounting method is proposed using a fine-needle capillary similar to that used for microinjection in cell biology. In this method, microcrystals are pulled up by capillary action or pipetting, and are held at the tip together with a small amount of cryoprotectant. The quality of the diffraction data using this method is comparable to that of data from conventional cryoloops. This solid apparatus is hopefully suitable for automation of microcrystal handling coupled with optical tweezers.

scholarly journals On effective and optical resolutions of diffraction data sets

2013 ◽  
Vol 69 (10) ◽  
pp. 1921-1934 ◽  
Author(s):  
Ludmila Urzhumtseva ◽  
Bruno Klaholz ◽  
Alexandre Urzhumtsev
Keyword(s):  
Diffraction Data ◽  
Minimum Distance ◽  
Optical Resolution ◽  
General Interest ◽  
Data Sets ◽  
Accurate Calculation ◽  
Data Set ◽  
X Ray ◽  
X Ray Crystallography ◽  
The Ideal

In macromolecular X-ray crystallography, diffraction data sets are traditionally characterized by the highest resolutiondhighof the reflections that they contain. This measure is sensitive to individual reflections and does not refer to the eventual data incompleteness and anisotropy; it therefore does not describe the data well. A physically relevant and robust measure that provides a universal way to define the `actual' effective resolutiondeffof a data set is introduced. This measure is based on the accurate calculation of the minimum distance between two immobile point scatterers resolved as separate peaks in the Fourier map calculated with a given set of reflections. This measure is applicable to any data set, whether complete or incomplete. It also allows characterizion of the anisotropy of diffraction data sets in whichdeffstrongly depends on the direction. Describing mathematical objects, the effective resolutiondeffcharacterizes the `geometry' of the set of measured reflections and is irrelevant to the diffraction intensities. At the same time, the diffraction intensities reflect the composition of the structure from physical entities: the atoms. The minimum distance for the atoms typical of a given structure is a measure that is different from and complementary todeff; it is also a characteristic that is complementary to conventional measures of the data-set quality. Following the previously introduced terms, this value is called the optical resolution,dopt. The optical resolution as defined here describes the separation of the atomic images in the `ideal' crystallographic Fourier map that would be calculated if the exact phases were known. The effective and optical resolution, as formally introduced in this work, are of general interest, giving a common `ruler' for all kinds of crystallographic diffraction data sets.

Design of a novel Peltier-based cooling device and its use in neutron diffraction data collection of perdeuterated yeast pyrophosphatase

2010 ◽  
Vol 43 (5) ◽  
pp. 1113-1120 ◽  
Author(s):  
Esko Oksanen ◽  
François Dauvergne ◽  
Adrian Goldman ◽  
Monika Budayova-Spano
Keyword(s):  
Data Collection ◽  
Neutron Diffraction ◽  
Diffraction Data ◽  
Catalytic Mechanism ◽  
Inorganic Pyrophosphatase ◽  
Neutron Diffraction Data ◽  
Cooling Device ◽  
Data Set ◽  
X Ray ◽  
X Ray Crystallography

H atoms play a central role in enzymatic mechanisms, but H-atom positions cannot generally be determined by X-ray crystallography. Neutron crystallography, on the other hand, can be used to determine H-atom positions but it is experimentally very challenging. Yeast inorganic pyrophosphatase (PPase) is an essential enzyme that has been studied extensively by X-ray crystallography, yet the details of the catalytic mechanism remain incompletely understood. The temperature instability of PPase crystals has in the past prevented the collection of a neutron diffraction data set. This paper reports how the crystal growth has been optimized in temperature-controlled conditions. To stabilize the crystals during neutron data collection a Peltier cooling device that minimizes the temperature gradient along the capillary has been developed. This device allowed the collection of a full neutron diffraction data set.

A batch-wise non-linear fitting and analysis tool for treating large X-ray diffraction data sets

2006 ◽  
Vol 39 (2) ◽  
pp. 262-266 ◽  
Author(s):  
R. J. Davies
Keyword(s):  
Diffraction Data ◽  
Operation Mode ◽  
Large Data ◽  
Scattering Data ◽  
Data Sets ◽  
Analysis Tool ◽  
Data Set ◽  
X Ray ◽  
Linear Fitting ◽  
Non Linear

Synchrotron sources offer high-brilliance X-ray beams which are ideal for spatially and time-resolved studies. Large amounts of wide- and small-angle X-ray scattering data can now be generated rapidly, for example, during routine scanning experiments. Consequently, the analysis of the large data sets produced has become a complex and pressing issue. Even relatively simple analyses become difficult when a single data set can contain many thousands of individual diffraction patterns. This article reports on a new software application for the automated analysis of scattering intensity profiles. It is capable of batch-processing thousands of individual data files without user intervention. Diffraction data can be fitted using a combination of background functions and non-linear peak functions. To compliment the batch-wise operation mode, the software includes several specialist algorithms to ensure that the results obtained are reliable. These include peak-tracking, artefact removal, function elimination and spread-estimate fitting. Furthermore, as well as non-linear fitting, the software can calculate integrated intensities and selected orientation parameters.

scholarly journals Protein microcrystallography using synchrotron radiation

IUCrJ ◽  
2017 ◽  
Vol 4 (5) ◽  
pp. 529-539 ◽  
Author(s):  
Masaki Yamamoto ◽  
Kunio Hirata ◽  
Keitaro Yamashita ◽  
Kazuya Hasegawa ◽  
Go Ueno ◽  
...  
Keyword(s):  
Synchrotron Radiation ◽  
Data Collection ◽  
Diffraction Data ◽  
Structure Determination ◽  
Structural Features ◽  
X Ray ◽  
Data Collection Strategy ◽  
Technological Developments ◽  
Novel Method

The progress in X-ray microbeam applications using synchrotron radiation is beneficial to structure determination from macromolecular microcrystals such as smallin mesocrystals. However, the high intensity of microbeams causes severe radiation damage, which worsens both the statistical quality of diffraction data and their resolution, and in the worst cases results in the failure of structure determination. Even in the event of successful structure determination, site-specific damage can lead to the misinterpretation of structural features. In order to overcome this issue, technological developments in sample handling and delivery, data-collection strategy and data processing have been made. For a few crystals with dimensions of the order of 10 µm, an elegant two-step scanning strategy works well. For smaller samples, the development of a novel method to analyze multiple isomorphous microcrystals was motivated by the success of serial femtosecond crystallography with X-ray free-electron lasers. This method overcame the radiation-dose limit in diffraction data collection by using a sufficient number of crystals. Here, important technologies and the future prospects for microcrystallography are discussed.

scholarly journals Neutron and high-resolution room-temperature X-ray data collection from crystallized lytic polysaccharide monooxygenase

2015 ◽  
Vol 71 (11) ◽  
pp. 1448-1452 ◽  
Author(s):  
John-Paul Bacik ◽  
Sophanit Mekasha ◽  
Zarah Forsberg ◽  
Andrey Kovalevsky ◽  
Jay C. Nix ◽  
...  
Keyword(s):  
High Resolution ◽  
Diffraction Data ◽  
Room Temperature ◽  
X Ray Diffraction ◽  
Lytic Polysaccharide Monooxygenase ◽  
Data Set ◽  
X Ray ◽  
Processing Enzymes ◽  
Bacteria And Fungi ◽  
Polysaccharide Monooxygenase

Bacteria and fungi express lytic polysaccharide monooxgyenase (LPMO) enzymes that act in conjunction with canonical hydrolytic sugar-processing enzymes to rapidly convert polysaccharides such as chitin, cellulose and starch to single monosaccharide products. In order to gain a better understanding of the structure and oxidative mechanism of these enzymes, large crystals (1–3 mm3) of a chitin-processing LPMO from the Gram-positive soil bacteriumJonesia denitrificanswere grown and screened for their ability to diffract neutrons. In addition to the collection of neutron diffraction data, which were processed to 2.1 Å resolution, a high-resolution room-temperature X-ray diffraction data set was collected and processed to 1.1 Å resolution in space groupP212121. To our knowledge, this work marks the first successful neutron crystallographic experiment on an LPMO. Joint X-ray/neutron refinement of the resulting data will reveal new details of the structure and mechanism of this recently discovered class of enzymes.

scholarly journals Diamonds in the rough: a strong case for the inclusion of weak-intensity X-ray diffraction data

2014 ◽  
Vol 70 (5) ◽  
pp. 1491-1497 ◽  
Author(s):  
Jimin Wang ◽  
Richard A. Wing
Keyword(s):  
Electron Density ◽  
Diffraction Data ◽  
Heavy Atom ◽  
Uniform Density ◽  
X Ray Diffraction ◽  
X Ray ◽  
Density Correlation ◽  
Atomic Models ◽  
Weak Intensity

Overwhelming evidence exists to show that the inclusion of weak-intensity, high-resolution X-ray diffraction data helps improve the refinement of atomic models by imposing strong constraints on individual and overall temperatureBfactors and thus the quality of crystal structures. Some researchers consider these data to be of little value and opt to discard them during data processing, particularly at medium and low resolution, at which individualBfactors of atomic models cannot be refined. Here, new evidence is provided to show that the inclusion of these data helps to improve the quality of experimental phases by imposing proper constraints on electron-density models during noncrystallographic symmetry (NCS) averaging. Using electron-density correlation coefficients as criteria, the resolution of data has successfully been extended from 3.1 to 2.5 Å resolution with redundancy-independent mergingRfactors from below 100% to about 310%. It is further demonstrated that phase information can be fully extracted from observed amplitudes throughde novoNCS averaging. Averaging starts with uniform density inside double-shelled spherical masks and NCS matrices that are derived from bound heavy-atom clusters at the vertices of cuboctahedrally symmetric protein particles.

scholarly journals Effect of Closed Loop Medication Administration on Drug Returns in Inpatient Facilities

2020 ◽  
Vol 8 (12) ◽  
Author(s):  
Eceberil Ozturk ◽  
Ilker Kose ◽  
Beytiye Elmas
Keyword(s):  
Patient Safety ◽  
Data Quality ◽  
Closed Loop ◽  
Medication Management ◽  
Medication Administration ◽  
Data Set ◽  
Return Rates ◽  
Conventional Drug ◽  
Turkish State

Medication management in inpatient facilities is a crucial issue for patient safety. In inpatient conventional drug management, a common problem relates to drugs prescribed and delivered to patients being returned to the pharmacy without reason for the return. When reasons are given, they are not often regularly and correctly recorded. Closed Loop Medication Administration (CLMA) protects patient safety by managing all processes, including intake of the drug to the hospital's stock, administering the drug to the patient, and disposal of unused drugs using technology. CLMA is known to contribute positively to patient safety. However, there is no study on the effect of CLMA on the return of non-administered drugs. This study aims to analyze the effect of CLMA on drug return rates and investigate the data quality of reasons for drug returns. The research was carried out in three inpatient clinics of a Turkish state hospital (Bolu İzzet Baysal Public Hospital) where the CLMA was implemented in May of 2017. The data set obtained from the hospital information system (HIS) is anonymized. The study showed a significant increase in drug return rates after CLMA, and the data quality of drug return reasons is also significantly improved. These results show that CLMA contributes positively to drug return rates and the data quality of drug return reason records.

scholarly journals Participant Recruitment Method Aiming at Service Quality in Mobile Crowd Sensing

2021 ◽  
Vol 2021 ◽  
pp. 1-14
Author(s):  
Weijin Jiang ◽  
Junpeng Chen ◽  
Xiaoliang Liu ◽  
Yuehua Liu ◽  
Sijian Lv
Keyword(s):  
Data Quality ◽  
Distance Constraint ◽  
Mobile Crowd Sensing ◽  
Constraint Factor ◽  
Data Set ◽  
Selection Scheme ◽  
Crowd Sensing ◽  
Participant Selection ◽  
Mobile Crowd

With the rapid popularization and application of smart sensing devices, mobile crowd sensing (MCS) has made rapid development. MCS mobilizes personnel with various sensing devices to collect data. Task distribution as the key point and difficulty in the field of MCS has attracted wide attention from scholars. However, the current research on participant selection methods whose main goal is data quality is not deep enough. Different from most of these previous studies, this paper studies the participant selection scheme on the multitask condition in MCS. According to the tasks completed by the participants in the past, the accumulated reputation and willingness of participants are used to construct a quality of service model (QoS). On the basis of maximizing QoS, two heuristic greedy algorithms are used to solve participation; two options are proposed: task-centric and user-centric. The distance constraint factor, integrity constraint factor, and reputation constraint factor are introduced into our algorithms. The purpose is to select the most suitable set of participants on the premise of ensuring the QoS, as far as possible to improve the platform’s final revenue and the benefits of participants. We used a real data set and generated a simulation data set to evaluate the feasibility and effectiveness of the two algorithms. Detailedly compared our algorithms with the existing algorithms in terms of the number of participants selected, moving distance, and data quality. During the experiment, we established a step data pricing model to quantitatively compare the quality of data uploaded by participants. Experimental results show that two algorithms proposed in this paper have achieved better results in task quality than existing algorithms.

Sign in / Sign up

Export Citation Format

Share Document