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Equipment & Training

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MSKC understands the evolving needs of Stanford scientists performing multidisciplinary research by providing a nurturing work environment. The lab fosters a collaborative and respectful working culture, welcoming everyone. In one spot, equipment and training are offered with a focus on the production, purification, biophysical analysis, and crystallization of biological molecules. Consult our funding opportunities for fundamental research - we help scientists enter the world of proteins to achieve their research goals.

Visit the Access & Reservations page for information of gaining access to the facility.

Visit the Rates page for information about current user fees.

Equipment and instrumentation

MSKC resources are shared. Researchers access them to perform experiments from getting the molecular sample to a variety of downstream applications including: protein expressionprotein purificationprotein analysisprotein crystallization, and additional resources.

Biophysical Analysis

Prometheus Panta

Molecular stability analysis measurements

Thermal unfolding nanoDSF

Size analysis DLS

Aggregation Backreflection

Sizing and aggregation propensity SLS

In-solution, immobilization-free, low sample consumption

Monolith Labelfree

Microscale Thermoforesis binding affinity measurements


Protein-small molecules (ions, nanoparticles)

Protein-nucleic acids (aptamers)

Protein-liposomes (vesicles)


In-solution, no surface attachment required, low sample consumption

Protein Purification


​Preparative purification system. Available columns:

Ion-exchange: Mono Q 5/50 GL and Mono S 5/50 GL.

Size-Exclusion: Superose 6 Increase, Superdex 75, and Superdex 200 Increase.

Miscellaneous: HiPrep 26/10 Desalting, HiPrep Butyl FF 16/10 and HiPrep Phenyl FF 16/10, Toyopearl Chelate.

Sorvall Lynx 4000 Centrifuge

Superspeed centrifuge

Rotors 6x 500 ml and 12x 50 ml capacity.

Max RCF 68,905 x g, max speed 24,000 rpm.

Tissue Homogeneizer and Cells Lysis

Fisher Model 705 Ultrasonic Sonicator processes 0.2 ml and up to 50 ml using three different microtips.

Spex SamplePrep Genolyte 1200 for optimal processing of small sample volume via bead beating. 

​Cell disruption, homogenization, DNA shearing, protein extraction, materials, powder, cements.

SDS-PAGE Electrophoresis

Electrophoretic separation of protein.

Mini gel tank system runs with precast acrylamide gels.

In-gel detection with blue staining solution. 

Bio-Rad CFX96 Real-Time PCR

Thermal shift assay using Sypro Orange readout.

Protein stability on different buffer conditions or with ligands.

Commercial buffer screens or home-made with our Art Robbins Scorpion.

GE Amersham Imager 600

Protein gel/membrane blot image acquisition instrument.

Chemiluminiscence, colorimetric epi-light, fluorescence trans-UV, epi-illumination, fluorescence red/green/blue epi light source.

Protein Expression

Tissue Culture

Biosafety cabinet: Labconco Purifier Class II, Type A2, for BSL1 work.

CO2-incubators: Fisher Reach-in and PHCbi CellQ equipped with shaking platforms.

Cell culture at 37℃ in a humidified environment of 5-8 % carbon dioxide.

MaxQ 8000 Orbital Shakers

Stacked refrigerated shakers each with a 8x 2 liter flask capacity.

37℃ for cell growth and 16℃ for low temperature induction.

27℃ reserved for baculovirus.

Protein Production Platform

UV-light sterilizable area for bacterial culture, manipulation, inoculum, media preparation, plating.

Other tools: electroporator, thermostated water bath, nanodrop for measuring DNA.

Protein Crystallization

Art Robbins Scorpion Liquid Handling Robot

Liquid handling robot volume range: 1.0 µl to 1,000 µl.

Accurate and programmable dispensing of pH-gradients, precipitant grids, concentration series.

Douglas Oryx8 Crystallization Robot

Automated crystallization screening robot using nanoliter dispensing.

Sitting-drop vapor-diffusion: concave-bottom Intelli Plate or flat-surface TTP 96-well plates.

288 crystal experiments per plate.

Crystal and additive screens available. Home-made screens with our Art Robbins Scorpion or the Douglas Oryx8.

Rumed 3000 Crystal Incubator

Vibration-free crystal growth incubators.

Set to one single-point temperature value at either 6 °C or 16 °C. 

Dedicated area available to grow crystals at ambient temperature.

Formulatrix RockImager2 UV-Vis Imager

Semi-automated crystal plate imager, crystal image searchable databank.​

Dual visible light, UV light tool to discriminate between protein and salt crystals.

Fast: 5-minutes per plate.

Discovery V12 Crystal Imaging Microscope

Large-surface, stereoscopic microscope for crystal manipulation.

Motorized 12:1 zoom controlled by the external touch panel SYCOP controller.

Camera for capturing crystal images.

Crystal Cryo-equipment

Crystal harvesting tools: cryo-pins, loops, cassettes, and dewars.

Shipping equipment: CX-100 shipping dewar, VHC35 storage dewar, LD5 transfer dewar and standard SSRL equipment for use with the SSRL Automated Mounting (SAM) system using SSRL cassettes.


Supporting macromolecular and small-molecule X-ray diffraction:

Synchrotron X-ray data collection.

Diffraction data analysis.

Validation and deposit of structures with the PDB.

Collaborations & Funding Opportunities

Sabrina Sanchez (Foothill College), Rasha Jameel (San Mateo College) STEM Student Interns in Action at MSKC

Open to Collaborations

MSKC has an excellent track-record fostering collaborations. Regardless of background and career stage, MSKC welcomes you to get your hands dirty with protein in a real-world laboratory setting. 

Do not hesitate contacting the MSKC staff for starting your journey in the protein world!    

Funding Opportunities


Training Program on Protein Expression, Purification, and Analysis of Biomolecules

To encourage more Stanford researchers to engage in structural biology and train them to better produce, purify, and characterize proteins, the Macromolecular Structure Knowledge Center (MSKC) at Sarafan ChEM-H is accepting proposals from Stanford scientists who would like to start or enhance a protein characterization project in their lab. Selected projects will receive personalized, hands-on training in a state-of-the-art facility and up to $7,500 in matching funds towards the project.


To apply, submit proposals through the SlideRoom application portal below by 11:59 p.m. on Friday, February 24, 2023.