Area detector design Part II. Application to a modular CCD-based detector for X-ray crystallography

Stanton, Martin; Phillips, W. A.; O'Mara, Daniel M.; Náday, I.; Westbrook, Edwin M.

doi:10.1016/0168-9002(93)90405-7

Cited by 20 publications

(16 citation statements)

References 6 publications

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“…All x-ray intensity data were measured at the Structural Biology Center undulator beamline (ID19) of the Advanced Photon Source using a mosaic charge-coupled devisebased x-ray detector (13). Data collection statistics are summarized in Table 1.…”

Section: Methodsmentioning

confidence: 99%

The crystal structure and mechanism of orotidine 5′-monophosphate decarboxylase

Appleby

Kinsland

Begley

et al. 2000

Proc. Natl. Acad. Sci. U.S.A.

172

216

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The crystal structure of Bacillus subtilis orotidine 5-monophosphate (OMP) decarboxylase with bound uridine 5-monophosphate has been determined by multiple wavelength anomalous diffraction phasing techniques and refined to an R-factor of 19.3% at 2.4 Å resolution. OMP decarboxylase is a dimer of two identical subunits. Each monomer consists of a triosephosphate isomerase barrel and contains an active site that is located across one end of the barrel and near the dimer interface. For each active site, most of the residues are contributed by one monomer with a few residues contributed from the adjacent monomer. The most highly conserved residues are located in the active site and suggest a novel catalytic mechanism for decarboxylation that is different from any previously proposed OMP decarboxylase mechanism. The uridine 5-monophosphate molecule is bound to the active site such that the phosphate group is most exposed and the C5-C6 edge of the pyrimidine base is most buried. In the proposed catalytic mechanism, the ground state of the substrate is destabilized by electrostatic repulsion between the carboxylate of the substrate and the carboxylate of Asp60. This repulsion is reduced in the transition state by shifting negative charge from the carboxylate to C6 of the pyrimidine, which is close to the protonated amine of Lys62. We propose that the decarboxylation of OMP proceeds by an electrophilic substitution mechanism in which decarboxylation and carbon-carbon bond protonation by Lys62 occur in a concerted reaction. O rotidine monophosphate (OMP, 1) decarboxylase catalyzes the final step in the de novo biosynthesis of uridine monophosphate (UMP, 2) (Eq. 1).In most prokaryotes, OMP decarboxylase is a dimer of identical subunits whereas in higher organisms, it is part of a bifunctional enzyme that also catalyzes the formation of OMP. Amino acid sequence comparisons suggest that monomeric and bifunctional OMP decarboxylases are structurally homologous with about a dozen residues conserved throughout all species. The enzyme accelerates this decarboxylation reaction by 10 17 and is the most proficient enzyme identified so far (1). OMP decarboxylase does not use any cofactors (2). Its mechanism is novel because the carbanion generated by carbon dioxide loss is localized in an sp 2 orbital perpendicular to the system of the pyrimidine. In all other decarboxylases, the carbanion is delocalized either into an adjacent carbonyl or into a covalently bound thiamin, pyridoxal, or pyruvoyl cofactor (3). Although several hypotheses have been advanced to explain how the enzyme stabilizes the carbanion intermediate, the mechanistic details of this reaction are currently unclear.Three mechanisms have been proposed for OMP decarboxylase (Scheme 1). In the first mechanism (zwitterion mechanism), protonation of the C2 carbonyl group would generate the zwitterion 3, in which the positive charge at N1 could stabilize the negative charge accumulating at C6 during the decarboxylation. This proposal was supported by a model study that dem...

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Section: Methodsmentioning

confidence: 99%

The crystal structure and mechanism of orotidine 5′-monophosphate decarboxylase

Appleby

Kinsland

Begley

et al. 2000

Proc. Natl. Acad. Sci. U.S.A.

172

216

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“…The critical design parameters of a protein crystallography detector are imaging area, dynamic range, readout time, sensitivity, and spatial resolution. 4,11 …”

Section: Design Requirementsmentioning

confidence: 99%

“…For imaging plate ͑IP͒ and charge coupled device ͑CCD͒ detectors, a large ͑ϳ10 5 ͒ dynamic range is sufficient to record most of the diffraction spots. 4,11,14 However, since a-Se is a direct conversion detector, there will be less scattering and less spreading of incoming x-rays. As a result, a strong diffraction spot will be confined to a smaller area asking for a higher dynamic range.…”

Section: Iib Dynamic Rangementioning

confidence: 99%

“…The imaging area of an ideal detector is the area required to collect all of the diffraction data to a specified resolution. 11 However, generally the first 100 orders of diffraction data contain useful information about the structure of protein crystal, 12 and therefore collecting those data with a large area ͑say, 20 cmϫ 20 cm͒ detector is sufficient to determine protein structure. The same field of view can be achieved by placing a smaller detector closer to the crystal.…”

Section: Iia Area Of the Detectormentioning

confidence: 99%

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Design and feasibility of active matrix flat panel detector using avalanche amorphous selenium for protein crystallography

et al. 2008

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Protein crystallography is the most important technique for resolving the three-dimensional atomic structure of protein by measuring the intensity of its x-ray diffraction pattern. This work proposes a large area flat panel detector for protein crystallography based on direct conversion x-ray detection technique using avalanche amorphous selenium (a-Se) as the high gain photoconductor, and active matrix readout using amorphous silicon (a-Si:H) thin film transistors. The detector employs avalanche multiplication phenomenon of a-Se to make the detector sensitive to each incident x ray. The advantages of the proposed detector over the existing imaging plate and charge coupled device detectors are large area, high dynamic range coupled to single x-ray detection capability, fast readout, high spatial resolution, and inexpensive manufacturing process. The optimal detector design parameters (such as detector size, pixel size, and thickness of a-Se layer), and operating parameters (such as electric field across the a-Se layer) are determined based on the requirements for protein crystallography application. The performance of the detector is evaluated in terms of readout time (<1 s), dynamic range (approximately 10(5)), and sensitivity (approximately 1 x-ray photon), thus validating the detector's efficacy for protein crystallography.

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“…A number of CCD-based x-ray detectors have been developed at Brandeis University for macromolecular crystallography. [1][2][3][4][5][6] The detector we describe here is based on these designs, with components and parameters optimized for screening mammography. The design is based on an array of cooled CCDs, each fiber optically coupled to a common phosphor.…”

Section: Introductionmentioning

confidence: 99%

Analysis of the detective quantum efficiency of a developmental detector for digital mammography

et al. 1999

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We are developing a modular detector for applications in full field digital mammography and for diagnostic breast imaging. The detector is based on a design that has been refined over the past decade for applications in x-ray crystallography [Kalata et al., Proc. SPIE 1345, 270-279 (1990); Phillips et al. ibid. 2009, 133-138 (1993), Phillips et al., Nucl. Instrum. Methods Phys. Rev. A 334, 621-630 (1993)]. The full field mammographic detector, currently undergoing clinical evaluation, is formed from a 19 cm x 28 cm phosphor screen, read out by a 2 x 3 array of butted charge-coupled device (CCD) modules. Each 2k x 2k CCD is optically coupled to the phosphor via a fiber optic taper with dimensions of 9.4 cm x 9.4cm at the phosphor. This paper describes the imaging performance of a two-module prototype, built using a similar design. In this paper we use cascaded linear systems analysis to develop a model for calculating the spatial frequency dependent noise power spectrum (NPS) and detective quantum efficiency (DQE) of the detector using the measured modulation transfer function (MTF). We compare results of the calculation with the measured NPS and DQE of the prototype. Calculated and measured DQEs are compared over a range of clinically relevant x-ray exposures and kVps. We find that for x-ray photon energies between 10 and 28 keV, the detector gain ranges between 2.5 and 3.7 CCD electrons per incident x-ray, or approximately 5-8 electrons per absorbed x ray. Using a Mo/Mo beam and acrylic phantom, over a detector entrance exposure range of approximately 10 to 80 mR, the volume under the measured 2-d NPS of the prototype detector is proportional to the x-ray exposure, indicating quantum limited performance. Substantial agreement between the calculated and measured values was obtained for the frequency and exposure dependent NPS and DQE over a range of tube voltage from 25 to 30 kVp.

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Area detector design Part II. Application to a modular CCD-based detector for X-ray crystallography

Cited by 20 publications

References 6 publications

The crystal structure and mechanism of orotidine 5′-monophosphate decarboxylase

The crystal structure and mechanism of orotidine 5′-monophosphate decarboxylase

Design and feasibility of active matrix flat panel detector using avalanche amorphous selenium for protein crystallography

Analysis of the detective quantum efficiency of a developmental detector for digital mammography

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