CryoEM Services for Protein Structure Determination

Understand the interplay between structure and function for your high-value drug target via our dedicated, end-to-end cryoEM workflow – and access specialist expertise to get the most out of your project.

Reduce the cost and time investment required to move your drug molecule to the clinic

CryoEM has now become an established method for high-resolution 3D protein structure determination.

Drug developers are turning to cryoEM to help enable effective structure-based drug design and the engineering of rational biologics for the most challenging targets. There are many instances where the technique is preferable to traditional approaches: 
  • The protein construct is hard to crystallize 
  • The target is conformationally dynamic
  • You have a large biomolecular complex
  • You work with membrane or membrane-associated proteins
  • A high- resolution map of an epitope is needed

Connect with the first and largest CRO to own and operate the necessary tools for full structure enablement

Our robust, fully flexible and expertise-driven cryoEM workflow supports the full range of study stages from sample characterization via negative stain through 3D reconstruction, model building and refinement.


As cryoEM specialists, our unique workflows and unrivalled expertise allows us to work with you to process your protein samples and vitrify them for imaging. 

Our cryoEM workflow: From initial sample to 3D reconstruction, model building and refinement 

Aggregation Analysis
Homogeneity Analysis
Vitrification Optimization
CryoEM Grid Screening
High Res Data Acquisition
3D Reconstruction
Aggregation Analysis

Negative Stain Screening

The first step in the workflow is a cursory examination to determine whether the sample is sufficiently pure and homogeneous for further, more detailed study by electron microscopy. At this stage, the sample should show evidence of well-defined, separated, high contrast particles of the expected size, with minimal or no aggregation. We have a long-standing expertise in the field, and we will work with the client to identify possible issues and provide suggestions on how to improve the sample.

Homogeneity Analysis

Negative stain with 2D classification

Once the sample has shown no or minimal aggregation, a detailed negative stain analysis performed to verify that the overall size, structure, oligomerization state, domain organization and conformational heterogeneity of the particles are consistent with those expected for the macromolecule of interest.  Sample grid preparation at this stage is carefully optimized to maximize the quality and resolution of the images with sufficient data acquired to perform 2D class averaging. Several of the resulting class averages must be clearly interpretable, with crisp features, limited disorder and flexibility, and limited oligomerization states to be prioritized for subsequent cryoEM study.

Vitrification Optimization

CryoEM grid preparation and screening

To obtain high resolution structural information, data must be collected using vitrified samples.  NIS has extensive, proven experience in sample vitrification and has developed a proprietary workflow for generating optimal and reproducible cryoEM grids. Samples will be vitrified either with the Vitrobot (ThermoFisher Scientific), a semi-automatic plunger, or using the Chameleon prototype (SPT Labtech), depending on sample conditions and results. Sample quality is iteratively assessed using in-house Glacios electron microscopes to ensure maximal workflow efficiency.
CryoEM Grid Screening

Grid prioritization & low-resolution data acquisition

 Screening of the grids with the Glacios microscope is used to identify the presence (or absence) of these potential issues that might prevent the client from obtaining high resolution structures. Grids are prioritized to maximize the likelihood that a structure of suitably high resolution can be achieve from data acquired on the Titan Krios instrument.  Grid screening can be combined with acquisition of an overnice dataset on the Glacios, which is subsequently used to obtain 2D classes (and sometimes a 3D reconstruction) to assess sample quality. 

High Res Data Acquisition

Data acquisition on in-house Krios microscopes

A high-resolution data collection requires optimal instrument conditions and highly experienced operators. To ensure consistency and stability during the data collection period, our microscope is carefully maintained resulting in less than 10% annual downtime.  Our automated data collection software (Leginon) allows us to run the microscope 24/7, and we have a web-based application that allows the client to remotely monitor the data collection in real-time. Pre-processing steps run in parallel with data acquisition so that both raw images and fully pre-processed micrographs are available for the client on completion of the run.  These can be transferred to the client's home computer for further processing or the 3D reconstruction completed by NIS.
3D Reconstruction

Data processing & 3D reconstruction

NIS offers a complete workflow for data processing that leads to a 3D reconstruction. This workflow includes particle picking, 2D classification, 3D classification, and 3D reconstruction. The many particles present in the images are initially classified into 2D classes.  Each class provides a different projection view of the macromolecule of interest, and these views can be mathematically combined to generate a 3D map.  The reconstructed map provides information for the entire volume of the particle, both surface features and internal morphology, and can reach atomic-level resolution. 

Customized Services

Fast, Flexible, Customized Services

In addition to project-based proposals, NIS offers custom service packages allowing you to get the most out of your specific program.

Training and Instrument access

Training & Instrument Access 

Our service offering combines a CRO approach with training and instrument access typically only accessible via academic and national laboratories. 

data acquisition only

Data Acquisition-Only Packages

As well as onsite training in sample preparation and data acquisition, we also offer data acquisition-only programs for users.

We currently house two Thermo Fisher Scientific Total Krios TEM microscopes equipped with Gatan K3 detectors, Gatan Quantum energy filters, and a Volta Phase plate on Krios1. 

We also house five Thermo Fisher Glacios cryo-TEM microscopes across our three facilities.
  • Installed across our locations to allow for local sample screening, preparation and analysis
  • A high-speed network will connect our facilities and the Krios microscopes for high-resolution data acquisition
We have delivery data for over 200 high-resolution data sets which have structurally enabled drug discovery pipelines for:
  • Integral membrane proteins (including ion channels, transporters, and GPCRs)
  • Large protein complexes
  • Molecular machines & dynamic systems
  • Gene editors
  • Epitopes
  • PROTACs


 Learn more about the different ways you can work with us through our Working With Us resource.

Request a CryoEM Consultation

Speak with a member of our scientific team about feasibility and sample considerations.

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