Compact HomeLab. 3D structure determination by protein crystallography. Low-maintenance, high-performance diffractometer

Transcription

1 Compact HomeLab 3D structure determination by protein crystallography Low-maintenance, high-performance diffractometer

2 The Compact HomeLab: Designed for productive, low-maintenance research in your own lab Transform the way you monitor your experiments Protein crystallography is not an easy experiment crystals tend to grow small and often diffract poorly. In the not too distant past, the demands of the crystallography experiment required a rotating anode X-ray source to produce data of high enough resolution to perform reasonable research in the home lab environment. Today, things have changed greatly due to concurrent advances in optics, X-ray Monitor your crystal, the instrument, and the diffraction quality anywhere on an iphone or ipad sources, detectors and software. It is now possible to configure a home lab protein crystallography system that will give you the ability to solve protein structures from diffraction data in a single software environment and with hardware that is as maintenance and worry-free as possible. Rigaku s Compact HomeLab will bring a new level of capabilities for protein crystallography to your lab. It has the industry s highest usable flux from a micro-focus sealed tube X-ray source, a comforting 3-year tube warranty, a new high-sensitivity Hybrid Pixel Array Detector (HPAD), optional remote ipad and iphone control and monitoring, and the unparalleled performance of HKL-3000R instrument control, data processing and solution structure. What more could you ask for? Micro-focus sealed tube source and optic are optimized to produce high flux in a beam less than 100 microns in diameter. 3-year tube warranty and a tube design that allows tubes to be changed in the field means one big thing your peace of mind. New PILATUS 200K HPAD that offers the highest sensitivity and dynamic range with the lowest read noise. The PILATUS 200K is also air-cooled so there s less maintenance compared to traditional CCDs. Kappa goniometer provides optimal data collection efficiency. HKL-3000R that combines instrument control, Rigaku s data collection strategy tool, data processing with HKL-2000, and a structure solution pipeline that uses industry standard software packages (CCP4, SHELX, ARP/wARP, COOT, SOLVE/RESOLVE, etc.). This combined software approach to crystallographic data collection and structure solution significantly accelerates the process of structure determination and on average minimizes the number of crystals, data sets and time required for structure solution. S-SAD phasing It is well known that S-SAD phasing requires accurate measurement of reflections. Moreover, many suggest the method requires very highly redundant data to extract the very weak 1 iphone and ipad are registered trademarks of Apple Inc., registered in the U.S. and other countries. HKL-3000R and HKL-2000 are registered trademarks of HKL Research, Inc.

3 Tough applications for the challenges of the real world S anomalous signal. Rigaku has shown that S-SAD phasing can be successful at medium, or even low, redundancy provided that the diffraction system is capable of accurate collection and measurement for diffraction data. This is true even for lower flux systems like the Compact HomeLab. Rigaku s standard Compact HomeLab now comes equipped with the PILATUS 200K detector. PILATUS detectors are true photon counting devices that combine the following features to make them the best commercially available detectors for protein crystallography: the highest sensitivity the lowest readout noise the fastest readout time and the lowest point spread function Whether you re collecting data for small or weakly diffracting samples or collecting data for S-SAD phasing, the Compact HomeLab system configured with a PILATUS detector ensures the most accurate data collection for your samples. S-SAD phasing of hen egg white lysozyme An example case of S-SAD phasing to solve the structure of hen egg white lysozyme, grown in the absence of NaCl is shown below. Gallus gallus lysozyme # sulfurs/total # residues 10/147 Degrees of data collected 180 Exposure time 15 sec./0.25 Space group P Resolution 1.7 Å Total # reflections (unique) (10354) Completeness (last shell) 92.1% (58.0%) Redundancy (last shell) 11.2 (2.9) <I/sig(I)> (last shell) 71.5 (9.5) Linear R merge 2.8% Resolution for heavy atoms search # sites found Site occupancy range 2.0 Å 8 (1 0.6) Correlation coefficients (all/weak) 24.95/8.99 FOM after DM 0.79 % residues auto-built/# waters added 95% R/R free after auto building 23.5/29.7 2Fo-Fc and DANO electron density maps contoured at 2σ for lysozyme, following auto-building with arp/warp 2

4 The Compact HomeLab redefi Efficiency in your lab How can you ensure that your students and researchers are working at the highest level of productivity? By providing them with the tools they need to perform their research as quickly as possible. Crystal to 3D structure with minimum effort Once you have harvested and mounted a crystal, the fun begins. Crystal centering can be achieved through the use of an ipad or iphone in close proximity to the goniometer. HKL-3000R provides the experimenter the ability to check the most important parameters defining the quality of the diffraction data, and gives insight into the particular steps of the structure elucidation process. In most cases, using the default settings of the program results in a highly complete model of a macromolecule. 3

5 nes your laboratory workflow You are no longer constrained to the laboratory In the past, the X-ray researcher was forced to spend too much time in the lab making sure that the experiment was going according to plan. With RigakuRemote, you have the ability to remotely monitor the status of a single crystal X-ray system from anywhere you can get an internet connection. It provides real-time updates of the state of your instrumentation, including video of the crystal and enclosure. Also included are current information about the scans being collected, and a JPEG view of the last diffraction image collected. Structure solution is not just for synchrotrons anymore The structure solution pipeline inherent to HKL-3000R seamlessly transfers output from one step to the next. Strategic stopping points are provided in the structure solution software to prevent the pitfalls commonly associated with black-box crystallography. In addition to its own internal database, the software communicates with standard databases like the PDB and SwissProt, as needed. 4

6 It is more that the sum of its p Rigaku s Compact HomeLab was designed for researchers who want a low-maintenance X-ray system with the ultimate in experimental flexibility. Providing those qualities requires a set of components that have been designed and optimized for the experiments that need to be run. X-ray beam optimized for small crystals The foundation of this system is the third generation Rigaku MicroMax -003, an integrated microfocus sealed tube generator with a specialized confocal multi-layer optic. The optic has been designed for the small crystals that are most frequently seen in today s structural biology labs. The beam size at the crystal is less than 100 μm in diameter, giving superior flux density for crystals smaller than 100 μm in size. The Compact HomeLab contains a specially designed multi-layer optic to optimize performance for the X-ray source and the PILATUS detector. The MicroMax-003, as optimized for the Compact HomeLab, has a beam diameter less than 100 μm at the crystal and a divergence of 7.3 mr. The flux through a 100 μm pinhole at the crystal position is 14 x 109 photons/sec/mm². The X-ray tube includes a 3-year warranty and requires little maintenance, which ensures that your time will be spent measuring samples instead of maintaining your X-ray source. The MicroMax-003 utilizes a 30 μm focal spot running at 30 watts of power. Superior long-term beam stability is maintained by a supplied cooling system. 5

7 arts It is synergy at its best Detector selected for performance The detector in the Compact HomeLab is the Dectris PILATUS 200K. This HPAD is a true photon counting detector that features: the highest sensitivity, the lowest readout noise, the highest dynamic range, the sharpest point spread function and the ability to collect data continuously. These combined detector characteristics make PILATUS detectors the best among today s commercially available detectors for crystallography. PILATUS detectors are the most efficient detectors when compared to other CMOS-based detectors. Moreover, they are ideal for the broadest range of crystal types. For example, the exceptionally low noise of PILATUS detectors ensures accurate measurement of reflections from weakly diffracting or small crystal samples. The high dynamic range of PILATUS detectors ensures that strong, low resolution reflections can be measured accurately without risk of saturation. This feature essentially eliminates the need for two data collection passes at long and short exposure times. PILATUS detectors feature extremely fast readout times, on the order of a few milliseconds. This translates to faster experiments and shutterless data collection the shutter opens once at the start of data collection and closes only at the end. This capability eliminates errors in the diffraction data originating from shutter timing and goniometer stop/starts, which are invariably associated with traditional data collection, and minimizes data collection time. Dectris PILATUS 200K detector The figure on the left illustrates the data collection efficiency comparison for HPAD and a conventional active pixel CMOS-based detector. The data collection efficiency measurement takes into account a number of detector characteristics, including detective quantum efficiency, the active measurement area and dead time (or shutter closed time). This comparison shows that the PILATUS 200K excels with regard to data collection efficiency compared to other commercially available CMOS-based detectors that rely on indirect detection of photons and/or are not amenable to shutterless data collection. 6

8 Compact HomeLab 3D structure determination by protein crystallography Rigaku Corporation and its Global Subsidiaries website: SYS_BRO_CHLv03 11_2013 Copyright Rigaku Corporation. All rights reserved.