NEW YORK STRUCTURAL BIOLOGY CENTER – INSTRUMENTATION
OVERVIEW
NYSBC offers unsurpassed instrumentation and expertise to the nine consortium member institutions, and is dedicated to developing, applying, integrating, and disseminating structural biology methods to all their faculty and trainees. Housing NIH-funded national centers, NYSBC is a nexus for biomedical researchers across the nation. This provide a unique benefit for the member institutions, as resources and facilities enable by these centers augments and expands what is available to users.
NYSBC also helps support the member institutions in building structural biology capabilities within their own institutions. For example, NYSBC can provide letters to support equipment grants to the NIH, individual PI grant proposals, and provide training to facility managers. In addition, workshops and classes held at NYSBC provide credit-earning graduate-level educational opportunities for trainees. By providing these opportunities, NYSBC enhances the research potential of the member institutions in a way that is unavailable to other universities, making the members more competitive in the fast-paced biomedical research environment.
CRYO-ELECTRON MICROSCOPY (SIMONS ELECTRON MICROSCOPY CENTER)
The Simons Electron Microscopy Center (SEMC) provides expertise and resources for understanding both molecular and cellular structures. Molecular structure determination is enabled by high-end transmission electron microscopes, direct detection cameras, and computational support for single particle analysis. Cellular structure determination is enabled by tomographic reconstructions using the transmission electron microscopes and a focused ion beam, scanning electron microscopes. Users from NYSBC member institutions can access SEMC equipment through the Members’ Electron Microscopy Center (MEMC).
Perhaps most importantly, MEMC users can access the rich training opportunities and expertise afforded by being collocated with several NIH funded centers and can make use of new methods and techniques being developed in the research and development efforts of NYSBC.
Electron microscopes:
- TFS Titan Krios G2 TEM 300keV, Gatan K3 direct detector plus BioQuantum energy filter.
- TFS Titan Krios G2 TEM 300keV, Cs corrector, Gatan K3 direct detector with BioQuantum energy filter.
- TFS Titan Krios G3i TEM 300keV, Gatan K3 direct detector with BioQuantum energy filter or TFS Falcon4i direct detector with Selectris energy filter.
- TFS Glacios TEM 200keV, Falcon3 direct detector or Falcon4i direct detector.
- Hitachi 7800 TEM 100keV, TVIPS CCD.
- TFS Arctis Cryo-Plasma Focused Ion Beam (cryo-PFIB) SEM for lamella preparation. (collaboration only)
- TFS Helios 5 Hydra DualBeam cryo-PFIB SEM for lamella preparation. (collaboration only)
Light Microscopes:
- ZEISS LSM 900 with Airyscan 2.
- Leica DMi8 inverted light microscope.
- Olympus BX43 light microscope.
Sample Preparation:
- SPTLabtech chameleon vitrification robot.
- 2x TFS Vitrobot Mark IV plunge freezer.
- 2x Leica GP2 plunge freezer.
- 1 Leica GP plunge freezer.
- 2x Gatan Solarus plasma cleaner.
- Leica ACE600 carbon coater.
- Wohlwend HPF Compact 01 High Pressure Freezer.
- Safematic CCU-010 high vacuum carbon coater.
- Bioforce UV ozone cleaner.
- Refeyn One(MP) Mass Photometer.
Research Computing:
- Live pre-processing (motion correction, CTF estimation) concurrent with a TEM session.
- Live data processing with cryoSPARC Live concurrent with a TEM session.
- With up to 40TB of temporary storage for each user and Globus services for secure data transfer.
Other equipment (additional expertise required):
- Mass Spectrometry Orbitrap 480 & Vanquish NEO system. (collaboration only)
- Syncell Microscoop for microscopy-guided photo-biotinylation. (collaboration only)
- EMCrafts Cube II tabletop SEM.
- Alveole Lab PRIMO micropatterning system.
- Leica EM UC6 ultramicrotome.
- Time resolved Spotiton 1.0. (collaboration only)
- Dataphysics OCA (optical contact angle goniometers and drop shape analysis systems).
NUCLEAR MAGNETIC RESONANCE
Spectrometers. NYSBC’S NMR instrumentation is truly world-class, with an array of equipment that can meet the need of almost any researcher and that allows experiments to be performed that are possible very few other places. In addition, routine measurements are accelerated as the appropriate instrument can be booked with little wait.
Eleven 11 Bruker NMR spectrometers available to users at member institutions:
1. 475 MHz NEO; Probes: TXI (room temperature)
BB-inverse (room temperature)
2. 500 MHz AV I; Probes: cryo TXI Z-gradient
3. 600 MHz AV III; Probes: 3.2mm HC(N/D) LTMAS DNP
2.5mm HFXY LTMAS DNP (Phoenix NMR)
1.9mm HCN LTMAS DNP
3.2mm HXY E-free MAS
4. 600 MHz AV III #2; Probes cryo H&F QCI Z-gradient
5. 700 MHz AV III; Probes: cryo H&F TCI Z-gradient
6. 750 MHz NEO; Probes: 1.9mm HXY MAS
3.2mm HCN E-free MAS
3.2mm HC(N/D) MAS
4.0mm HFX MAS
4.0mm HCN HRMAS
7. 800 MHz NEO; Probes: cryo TCI Z-gradient
cryo H&F TCI Z-gradient
1.7mm cryo TCI Z-gradient
1.9mm Tri-Gamma MAS
3.2mm HCN Cryo-MAS**
8. 800 MHz AV III HD; Probes: cryo TCI Z-gradient
cryo TXO Z-gradient
9. 800 MHz AV I; Probes: cryo TXI Z-gradient
10. 900 MHz NEO; Probes: cryo TCI Z-gradient
0.6mm HFXY MAS (Phoenix NMR, 2025)
1.2mm HFXY MAS (Phoenix NMR)
1.6mm HXY Bio MAS (Phoenix NMR)
1.3mm HC(N/D) Fast MAS
2.5mm HXY MAS (Black Fox)
3.2mm HCN E-free MAS
3.2mm HX MAS
4.0mm HCN HRMAS
11. 900 MHz AV I; Probes: cryo TCI Z-gradient
** First of its kind to be installed in the US.
Other unique equipment: In addition to the ten spectrometers, the NYSBC NMR department offers access to unique equipment that expands the range of experiments that can be performed:
- A Field Cycling Technologies shuttle system is installed on the 700 MHz NMR spectrometer.
- An ICARUS pressure-jump instrument in installed on an 800 MHz NMR spectrometer.
- A portable Daedelus high-pressure instrument can be used on any of the above spectrometers.
- A refrigerated Sample Jet (480 samples) sample changer for screening on an 800 MHz NMR spectrometer.
- A sample case sample changer for remote operation on an 800 MHz & 600 MHz NMR spectrometers.
- A developmental rapid-freeze quench apparatus for preparing samples for solid-state NMR spectroscopy.
X-RAY CRYSTALLOGRAPHY
NYX Beamline at NSLS-II: NYSBC designed, built, and now operates the NYX beamline at Brookhaven National Laboratory’s NSLS-II synchrotron. Combined with the 10,000-fold increase in X-ray brightness at NSLS-II, this improved instrumentation has made feasible experiments that were previously impossible. In the last several years, NYSBC has invested in this beamline to bring it to the cutting edge of crystallography. Recent improvements in the experimental equipment have resulted in an increase in throughput, higher reliability, improved sample visualization and modern experimental capabilities that are expected from researchers at synchrotron beamlines. NYX is fully available to users from all NYSBC member institutions. Equipment includes:
- The NYX beamline features a an in-vacuum undulator with an 18 mm period to generate the X-ray beam. The X-ray bam has an energy range from 7-14 keV with a 25 μm FWHM spot size.
- The sample mounting robot is an Irelec ISARA2 which provides a typical sample exchange time near 15 seconds.
- The detector at NYX is an Eiger2 XE 9M.
- The goniometer is an Arinax MD2-S (plate holder coming 2024).
SPECIAL PROJECTS GROUP
The Special Projects Group (SPG) provides a full gene-to-structure pipeline dedicated to protein research with a full range of services from target selection, cloning, expression, purification, crystallization to structure determination. The SPG brings over 15 years of experience in protein production and structure determination to assist and collaborate with users at all levels.
SPG personnel are regular users of NYSBC’s NYX beamline for X-ray crystallography, but also have experience with structure determination by cryoEM, utilizing microscopes at NYSBC.
- Full range of basic molecular biology equipment for cloning, protein expression, and purification.
- Expertise in bacterial, insect, and mammalian cell gene expression.
- Equipment for Protein Purification and Analysis:
- Cytiva AKTAxpress chromatography system (4)
- Cytiva AKTA Pure chromatography system (1)
- Cytiva AKTA Purifier 10 chromatography system (1)
- Cytiva AKTA FPLC chromatography system (1)
- full assortment of Cytiva chromatography columns (size exclusion, affinity, ion exchange, etc)
- Thermo Scientific NanoDrop 2000c spectrophotometer (1)
- NanoTemper Tycho NT.6 (1)
- NanoTemper Monolith NT.115 MST (1)
- NanoTemper Monolith NT.LabelFree MST (1)
- Equipment for Crystallization and X-ray Structure Determination
- Formulatrix NT8 drop setting robot
- Formulatrix Formulator 10 crystallization screen builder
- Formulatrix Rock Imager 1000
- Olympus SZX12 microscope
- Linux workstations with up-to-date crystallography software
- Rapid access to NSLS-II NYX beamline at BNL