R. Herbst

High-resolution protein structure determination by serial femtosecond crystallography

Size Matters Less X-ray crystallography is a central research tool for uncovering the structures of proteins and other macromolecules. However, its applicability typically requires growth of large crystals, in part because a sufficient number of molecules must be present in the lattice for the sample to withstand x-ray—induced damage. Boutet et al. (p. 362, published online 31 May) now demonstrate that the intense x-ray pulses emitted by a free-electron laser source can yield data in few enough exposures to uncover the high-resolution structure of microcrystals. A powerful x-ray laser source can probe proteins in detail using much smaller crystals than previously required. Structure determination of proteins and other macromolecules has historically required the growth of high-quality crystals sufficiently large to diffract x-rays efficiently while withstanding radiation damage. We applied serial femtosecond crystallography (SFX) using an x-ray free-electron laser (XFEL) to obtain high-resolution structural information from microcrystals (less than 1 micrometer by 1 micrometer by 3 micrometers) of the well-characterized model protein lysozyme. The agreement with synchrotron data demonstrates the immediate relevance of SFX for analyzing the structure of the large group of difficult-to-crystallize molecules.

Energy-dispersive X-ray emission spectroscopy using an X-ray free-electron laser in a shot-by-shot mode

The ultrabright femtosecond X-ray pulses provided by X-ray free-electron lasers open capabilities for studying the structure and dynamics of a wide variety of systems beyond what is possible with synchrotron sources. Recently, this “probe-before-destroy” approach has been demonstrated for atomic structure determination by serial X-ray diffraction of microcrystals. There has been the question whether a similar approach can be extended to probe the local electronic structure by X-ray spectroscopy. To address this, we have carried out femtosecond X-ray emission spectroscopy (XES) at the Linac Coherent Light Source using redox-active Mn complexes. XES probes the charge and spin states as well as the ligand environment, critical for understanding the functional role of redox-active metal sites. Kβ1,3 XES spectra of MnII and Mn2III,IV complexes at room temperature were collected using a wavelength dispersive spectrometer and femtosecond X-ray pulses with an individual dose of up to >100 MGy. The spectra were found in agreement with undamaged spectra collected at low dose using synchrotron radiation. Our results demonstrate that the intact electronic structure of redox active transition metal compounds in different oxidation states can be characterized with this shot-by-shot method. This opens the door for studying the chemical dynamics of metal catalytic sites by following reactions under functional conditions. The technique can be combined with X-ray diffraction to simultaneously obtain the geometric structure of the overall protein and the local chemistry of active metal sites and is expected to prove valuable for understanding the mechanism of important metalloproteins, such as photosystem II.

The CSPAD megapixel x-ray camera at LCLS

The Linear Coherent Light Source (LCLS), a free electron laser operating from 250eV to10keV at 120Hz, is opening windows on new science in biology, chemistry, and solid state, atomic, and plasma physics1,2. The FEL provides coherent x-rays in femtosecond pulses of unprecedented intensity. This allows the study of materials on up to 3 orders of magnitude shorter time scales than previously possible. Many experiments at the LCLS require a detector that can image scattered x-rays on a per-shot basis with high efficiency and excellent spatial resolution over a large solid angle and both good S/N (for single-photon counting) and large dynamic range (required for the new coherent x-ray diffractive imaging technique3). The Cornell-SLAC Pixel Array Detector (CSPAD) has been developed to meet these requirements. SLAC has built, characterized, and installed three full camera systems at the CXI and XPP hutches at LCLS. This paper describes the camera system and its characterization and performance.

X‐ray detectors at the Linac Coherent Light Source

This paper offers an overview of area detectors developed for use at the Linac Coherent Light Source (LCLS) with particular emphasis on their impact on science. The experimental needs leading to the development of second-generation cameras for LCLS are discussed and the new detector prototypes are presented.

The Cornell-SLAC pixel array detector at LCLS

The Cornell-SLAC pixel array detector (CSpad) is a general-purpose integrating hybrid pixel x-ray camera developed for use at the Linear Coherent Light Source (LCLS) x-ray free electron laser at the SLAC National Accelerator Laboratory (SLAC). The detector has a full well capacity of about 2.Sk photons in low-gain mode and a SIN of about 6 in high-gain mode. Its 2.3M pixels are read out at 120 Hz. The detector comprises 32 500μm silicon sensors bump-bonded to 64 185×194-pixel ASICs. The pixel size is 110μm. The water-cooled detector quadrants can be radially moved in-situ to vary the beam aperture. SLAC has built, calibrated, and optimized three complete camera systems based on a sensor and ASIC designed by Cornell. The camera is read out by a DAQ system which provides extensive online monitoring and prompt analysis capabilities. We have also built a dozen smaller cameras in a portable form-factor for use in confined spaces and for ease of development, testing, and deployment. Through 2012 user experiments have taken almost a petabyte of data with these detectors in a variety of applications. We have extensively tested the detector at synchrotrons and with an x-ray tube, in addition to commissioning tests at the LCLS, investigating linearity, cross-talk, homogeneity, and radiation hardness. The SLAC detector group is deploying improved support infrastructure and an updated ASIC and electronics based on this experience. This paper describes the instrument, its calibration and performance, and presents preliminary results from the updated camera.

Detector Development for the Linac Coherent Light Source

Since it began operations in 2009, the Linac Coherent Light Source (LCLS) has opened a new and dynamic frontier in terms of light sources and their associated science [1, 2]. An increase in brightness by a factor of a billion over pre-existing synchrotrons, in combination with ultra-brief pulses of coherent X-rays, is ushering in a new era in the photon sciences. Pulses with durations of 50 fs under standard conditions and below 10 fs with a reduced energy per bunch are possible. Over 1013 or 1012 X-rays per pulse can be generated at the upper and lower ends of the X-ray energy range of 285 eV to 9600 eV. One of the unique machine parameters is its strobe-like time structure, where single ultra-brief pulses are delivered at a repetition rate of 120 Hz. The above characteristics represent a singular environment in which to operate detectors and demand the development of a new class of high-frame-rate camera systems.

Design of the SLAC RCE Platform: A general purpose ATCA based data acquisition system

The SLAC RCE platform is a general purpose clustered data acquisition system implemented on a custom ATCA compliant blade, called the Cluster On Board (COB). The core of the system is the Reconfigurable Cluster Element (RCE), which is a system-on-chip design based upon the Xilinx Zynq family of FPGAs, mounted on custom COB daughter-boards. The Zynq architecture couples a dual core ARM Cortex A9 based processor with a high performance 28nm FPGA. The RCE has 12 external general purpose bi-directional high speed links, each supporting serial rates of up to 12Gbps. 8 RCE nodes are included on a COB, each with a 10Gbps connection to an on-board 24-port Ethernet switch integrated circuit. The COB is designed to be used with a standard full-mesh ATCA backplane allowing multiple RCE nodes to be tightly interconnected with minimal interconnect latency. Multiple shelves can be clustered using the front panel 10-gbps connections. The COB also supports local and inter-blade timing and trigger distribution. An experiment specific Rear Transition Module adapts the 96 high speed serial links to specific experiments and allows an experiment-specific timing and busy feedback connection. This coupling of processors with a high performance FPGA fabric in a low latency, multiple node cluster allows high speed data processing that can be easily adapted to any physics experiment. RTEMS as well as Linux are ported to the module. The RCE has been used or is the baseline for several current and proposed experiments (LCLS, HPS, LSST, ATLAS-CSC, LBNE, DarkSide, ILC-SiD, etc).

Design and characterization of the ePix10k prototype: A high dynamic range integrating pixel ASIC for LCLS detectors

ePix10k is a variant of a novel class of integrating pixel ASICs architectures optimized for the processing of signals in second generation LINAC Coherent Light Source (LCLS) X-Ray cameras. The ASIC is optimized for high dynamic range application requiring high spatial resolution and fast frame rates. ePix ASICs are based on a common platform composed of a random access analog matrix of pixel with global shutter, fast parallel column readout, and dedicated sigma-delta analog to digital converters per column. The ePix10k variant has 100um×100um pixels arranged in a 176×192 matrix, a resolution of 140e- r.m.s. and a signal range of 3.5pC (10k photons at 8keV). In its final version it will be able to sustain a frame rate of 2kHz. A first prototype has been fabricated and characterized. In this paper the ASIC performance in terms of noise, linearity, uniformity and cross-talk are presented, together with preliminary measurements with bump bonded sensors.

ePix: A class of front-end ASICs for second generation LCLS integrating hybrid pixel detectors

ePix is a novel class of ASICs architectures based on a common platform optimized for the processing of signals in second generation LCLS cameras. The platform architecture is composed of a random access analog matrix of pixels with a global shutter, fast parallel column readout, and dedicated sigma-delta analog to digital converters per column. It also implements a dedicated control interface and all the required support electronics to perform configuration, calibration, and readout of the matrix. Based on this platform a class of front-end ASICs and several camera modules are under development, each utilizing specific pixel architectures, to meet varying requirements. This approach reduces development time and expands the possibility of integration of detector modules in size, shape or functionality as different modules could be assembled in the same camera. The ePix platform is currently under development together with two integrating pixel architectures: ePix100 optimized for ultra-low noise applications and ePix10k optimized instead for high dynamic range applications.

eLine100: A front end ASIC for LCLS detectors in low noise applications

eLine100 is a fast-frame 96-channel readout ASIC for SLAC Linac Coherent Light Source (LCLS) detectors. The circuit has been designed to integrate the charge from high-capacitance 2D sensors with rolling shutter and 1D sensors. It has a noise floor of 55 e- + 8 e-/pF r.m.s. at room temperature and it is suitable for applications requiring resolutions on the order of 100 e- r.m.s. and signals up to 120 photons/pixel/pulse at 8 keV ( 260 ke-). 2D sensors with a rolling shutter like the X-ray Charge Pump Sensor (XCPS), for which the ASIC has been optimized, present many pixels which are bussed on the same readout line. This characteristic, together with the fixed LCLS beam period, impose limitations on the time available for the read out of each pixel. Given the periodic structure of the LCLS beam, the ASIC developed for this application is a time-variant system, providing a two-stage low-noise charge integration, filtering, correlated double sampling and a processing speed of up to 250 k pixel/s on each channel. To cope with the required input range, a charge pump scheme has been implemented using an asynchronous zero-balance measurement method. It provides on-chip 1-bit coarse analog-to-digital conversion of the integrated charge. The residual charge is sampled using correlated double sampling into an analog memory, multiplexed and measured with the required resolution by an external ADC. In this paper, the ASIC architecture and performances are presented.