A computer-linked cathode-ray tube microdensitometer for X-ray crystallography

Arndt, U. W.; Crowther, R. Anthony; Mallett, J F W

doi:10.1088/0022-3735/1/5/303

Cited by 76 publications

(30 citation statements)

References 5 publications

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“…It is defined as: withlh = LL Ih.i h Arndt 4 introduced R svrn as a reliability indicator for data collected by precession photography, where R svrn was specifically summed over symmetry-related intensities on the same film, and R sca ' calculated in an analogous fashion, reported the agreement of identical reflections measured on different films. As oscillation photography was introduced, so that symmetry related reflections were not commonly on the same film, it appears that the original R svrn and R sca were combined into the present day R svlTI which is summed over all observed equivalent reflections.…”

mentioning

confidence: 99%

Improved R-factors for diffraction data analysis in macromolecular crystallography

Diederichs

Karplus

1997

Nat Struct Mol Biol

853

635

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The quantity R sym (also called R merge ) is almost universally used for describing X-ray diffraction data quality. Here, we prove that R sym is seriously flawed, because it has an implicit dependence on the redundancy of the data. A corrected R-factor, R meas ' is introduced as the equivalent robust indicator of data consistency. In addition, we introduce R mrgd , an R-factor that reflects the gain in accuracy upon averaging ofequivalent reflections, as a useful indicator of the quality of reduced data. These new data quality indicators better reveal the benefits of highly redundant data and should stimulate improvements in data quality through increased merging of data from multiple crystals.R syrn (sometimes called Rrnerge)' is the most widespread statistic used to indicate data quality for rnacromolecular crystallographyl,2, and with the advent of area detectors for small molecule crystallography it is a standard quality indicator for that field as welP. It is defined as:Arndt 4 introduced R svrn as a reliability indicator for data collected by precession photography, where R svrn was specifically summed over symmetry-related intensities on the same film, and R sca ' calculated in an analogous fashion, reported the agreement of identical reflections measured on different films. As oscillation photography was introduced, so that symmetry related reflections were not commonly on the same film, it appears that the original R svrn and R sca were combined into the present day R svlTI which is summed over all observed equivalent reflections. 'R svrn is commonly used to guide decisions during data reduction,' such as determining to what resolution data are reliable, and whether two crystals are isomorphous, so that their data should be merged together. A single R svrn value is generally reported in publications to summarize the data quality. Overall R SVlTI values of <5%, 5-10%, 10-20% and >20% are taken to indicate good, usable, marginal, and questionable quality data respectively2.Here, we present empirical and mathematical analyses proving that R syrn is an inherently unreliable indicator of data quality. We also present alternate indicators that provide more robust measures of the quality of the individual measurements as well as of the final reduced data set. We expect that the application of the ideas described here will result in improved primary data quality, and ultimately in more accurate macromolecular structures. Experimental dataThe analyses presented here hold true for diffraction data measured with various detector/software combinations, but for simplicity, we present analyses based on three sets of data collected from crystals of the enzyme urease with Cys 319 from the a-chain mutated to Alas. These crystals are isomorphous with wild-type urease and grow in space group 12[3 with a=170.8 A6,7. Independent 2 A resolution data sets were collected from each of three crystals which had been soaked at pH values of 6.5, 7.5 and 8.5; these are designated Ure_1, Ure_2, and Ure_3 respectively. Difference Four...

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confidence: 99%

Improved R-factors for diffraction data analysis in macromolecular crystallography

Diederichs

Karplus

1997

Nat Struct Mol Biol

853

635

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“…, where I i (hkl) is the observed intensity and <I(hkl)> is the average intensity of multiple observations from symmetry-related reflections [52].…”

Section: Overall Structure Of Dr1998mentioning

confidence: 99%

Structure of the monofunctional heme catalase DR1998 from Deinococcus radiodurans

et al. 2014

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Deinococcus radiodurans is an aerobic organism with the ability to survive under conditions of high radiation doses or desiccation. As part of its protection system against oxidative stress, this bacterium encodes three monofunctional catalases. The DR1998 catalase belongs to clade 1, and is present at high levels under normal growth conditions. The crystals of DR1998 diffracted very weakly, and the merged diffraction data showed an R sym of 0.308. Its crystal structure was determined and refined to 2.6 Å. The four molecules present in the asymmetric unit form, by crystallographic symmetry, two homotetramers with 222 point‐group symmetry. The overall structure of DR1998 is similar to that of other monofunctional catalases, showing higher structural homology with the catalase structures of clade 1. Each monomer shows the typical catalase fold, and contains one heme b in the active site. The heme is coordinated by the proximal ligand Tyr369, and on the heme distal side the essential His81 and Asn159 are hydrogen‐bonded to a water molecule. A 25‐Å‐long channel is the main channel connecting the active site to the external surface. This channel starts with a hydrophobic region from the catalytic heme site, which is followed by a hydrophilic region that begins on Asp139 and expands up to the protein surface. Apart from this channel, an alternative channel, also near the heme active site, is presented and discussed. Database Coordinates and structure factors have been deposited in the Protein Data Bank in Europe under accession code http://www.rcsb.org/pdb/search/structidSearch.do?structureId=4CAB

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“…0.05-~m2 areas, containing ~650 unit cells, were microdensitometered (Arndt et al, 1968) at the equivalent of 4.4 if intervals, and the resulting 512 x 512 arrays were transformed on an IBM 370/165 computer. The digital transforms usually contained additional reflections not observed in the optical patterns.…”

Section: (C) Optical Diffractionmentioning

confidence: 99%