Outlier Treatment in Data Merging

Blessing, Robert H.

doi:10.1107/s0021889896014628

Cited by 1,375 publications

(676 citation statements)

References 9 publications

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“…In the second method, data sets for each individual wavelength (edge and peak) were used to calculate anomalous differences which were then converted to E values. Data sets were scaled and processed with the programs LOCSCL and LEVY (38) and renormalized E values derived from the anomalous differences were calculated by the program DIFFE (39).…”

Section: Methodsmentioning

confidence: 99%

Structure of Human Adenosine Kinase at 1.5 Å Resolution^,

1998

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Adenosine kinase (AK) is a key enzyme in the regulation of extracellular adenosine and intracellular adenylate levels. Inhibitors of adenosine kinase elevate adenosine to levels that activate nearby adenosine receptors and produce a wide variety of therapeutically beneficial activities. Accordingly, AK is a promising target for new analgesic, neuroprotective, and cardioprotective agents. We determined the structure of human adenosine kinase by X-ray crystallography using MAD phasing techniques and refined the structure to 1.5 Å resolution. The enzyme structure consisted of one large R/ domain with nine -strands, eight R-helices, and one small R/ -domain with five -strands and two R-helices. The active site is formed along the edge of the -sheet in the large domain while the small domain acts as a lid to cover the upper face of the active site. The overall structure is similar to the recently reported structure of ribokinase from Escherichia coli [Sigrell et al. (1998) Structure 6, 183-193]. The structure of ribokinase was determined at 1.8 Å resolution and represents the first structure of a new family of carbohydrate kinases. Two molecules of adenosine were present in the AK crystal structure with one adenosine molecule located in a site that matches the ribose site in ribokinase and probably represents the substrate-binding site. The second adenosine site overlaps the ADP site in ribokinase and probably represents the ATP site. A Mg 2+ ion binding site is observed in a trough between the two adenosine sites. The structure of the active site is consistent with the observed substrate specificity. The active-site model suggests that Asp300 is an important catalytic residue involved in the deprotonation of the 5′-hydroxyl during the phosphate transfer.Adenosine kinase (ATP, adenosine 5′-phosphotransferase, EC 2.7.1.20) catalyzes the phosphorylation of ribofuranosylcontaining nucleoside analogues at the 5′-hydroxyl using ATP or GTP as the phosphate donor. Tissue distribution studies indicate that adenosine kinase (AK) is the most abundant nucleoside kinase in mammals with AK activity in humans and monkeys expressed at the highest levels in liver, kidney, and lung and at intermediate levels in the brain, heart, and skeletal muscle (1, 2). AK exhibits a relatively broad substrate specificity tolerating modifications in both the sugar and base moieties (3). Accordingly, numerous nucleoside antiviral and anticancer drugs are AK substrates and consequently undergo rapid phosphorylation in vivo to the 5′-monophosphate. In many cases, the monophosphate is subsequently converted by other kinases to the triphosphate which functions as the active metabolite. Examples include ribavirin (4) and mizoribine (5).The physiological function of AK is associated with the regulation of extracellular adenosine levels and the preservation of intracellular adenylate pools (6

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Section: Methodsmentioning

confidence: 99%

Structure of Human Adenosine Kinase at 1.5 Å Resolution^,

1998

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“…controlled by the Collect [35] software package and an Oxford Cryosystem N2 open flow cryostat at 120(2) K. The data were processed using Denzo [36] and semi-empirical absorption corrections were applied using SORTAV [37,38]. The crystallographic data collection for compound 9 was performed on a Rigaku AFC12 diffractometer equipped with an enhanced sensitvity (HG) Saturn724+ CCD detector mounted at rhe window of a FR-E+ SuperBright rotating anode generator (Mo K radiation ( = 0.71075Å )) equipped with VariMax HF (High Flux) optics at 100(2) K. Software package CrystalClear-SM Expert 2.0 r 13 [39] was used for the cell determination, data collection, integration, scaling and absorption correction.…”

Section: X-ray Crystallographymentioning

confidence: 99%

Synthesis and X-ray structural studies of pentaborate(1−) salts containing substituted imidazolium cations

2014

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The preparation of [NMC][B5O6(OH)4] {NMC = 2-MeC3N2H4 (3),1-MeC3N2H4 (4), 4-MeC3N2H4 (5), 1,2-Me2C3N2H3 (6), 1,2,3-Me3C3N2H2 (7), 1-EtC3N2H4 (8), 2-EtC3N2H4 (9), 2-Et-4-MeC3N2H3 (10) 1-Et-3-MeC3N2H3 (11) and 2-i PrC3N2H4 (12)} salts are reported. Compounds were characterized by spectroscopy (NMR and IR) and by single crystal XRD (6, 7, 9, 10, 12) studies. All structures show extensive H-bonded networks and 7 displays the first example of reciprocal paired  anion-anion interactions.These are facilitated by the pentaborate boroxole rings being significantly distorted

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“…meter with rotating anode (λ ) 0.710 73 Å). The data were merged using the program SortAV, 25 resulting in 3378 unique reflections (Rint ) 0.036). An absorption correction was not considered necessary.…”

Section: Methodsmentioning

confidence: 99%

“…Apart from the major H(6) resonance at 8. 25 ppm, additional resonances with low intensity (<5%) are observable, which point to the presence of minor amounts of (R)-3b (δ H(6) ) 8.30 and 8.16 ppm) and its enantiomer (S)-3b in solution.…”

Section: Self-assembly Of Chiral Diamine-chelated Aryllithiumsmentioning

confidence: 98%

Diastereoselective Self-Assembly of Chiral Diamine-Chelated Aryllithiums to Dimeric Aggregates

et al. 2004

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, and [LiC6H4(CH(Me)N(Me)CH2CH2NMe2-(rac))-2]2 ((rac)-3b) were synthesized and characterized in the solid state and in solution. X-ray crystallographic studies of 2b and (R)-3b and molecular weight determinations of 2b, (R)-3b, and (rac)-3b by cryoscopy in benzene showed that, both in the solid state and in apolar, noncoordinating solvents such as benzene, these compounds exist as discrete dimeric aggregates. For (R)-3b and (rac)-3b the aggregation process of two monomeric aryllithium units to one dimer is highly diastereoselective.

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Outlier Treatment in Data Merging

Abstract: Experience with a variety of diffraction data-reduction problems has led to several strategies for dealing with mismeasured outliers in multiply measured data sets. Key features of the schemes employed currently include outlier identification based on the val-

Cited by 1,375 publications

References 9 publications

Structure of Human Adenosine Kinase at 1.5 Å Resolution^,

Structure of Human Adenosine Kinase at 1.5 Å Resolution^,

Synthesis and X-ray structural studies of pentaborate(1−) salts containing substituted imidazolium cations

Diastereoselective Self-Assembly of Chiral Diamine-Chelated Aryllithiums to Dimeric Aggregates

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Outlier Treatment in Data Merging

Abstract: Experience with a variety of diffraction data-reduction problems has led to several strategies for dealing with mismeasured outliers in multiply measured data sets. Key features of the schemes employed currently include outlier identification based on the val-

Cited by 1,375 publications

References 9 publications

Structure of Human Adenosine Kinase at 1.5 Å Resolution,

Structure of Human Adenosine Kinase at 1.5 Å Resolution,

Synthesis and X-ray structural studies of pentaborate(1−) salts containing substituted imidazolium cations

Diastereoselective Self-Assembly of Chiral Diamine-Chelated Aryllithiums to Dimeric Aggregates

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Product

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About

Structure of Human Adenosine Kinase at 1.5 Å Resolution^,

Structure of Human Adenosine Kinase at 1.5 Å Resolution^,