Protein crystallography facility

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X-ray crystallography technique helps to determine biological macromolecule structures that provide a detailed understanding of the interactions occurring at the molecular levels. Structure based drug design, study of protein-ligand interactions and structure-function relationships are the major fields where X-ray crystallography acts as a major tool.

Make and Model

Detector : Rigaku, R-Axis IV++

Available mode for use

  • Screen protein and DNA/RNA crystals for preliminary diffraction to improve quality

  • Solve structure of know protein structures with ligands (molecular replacement) (inhibitors, substrates, nucleic acids etc.)

  • Solve structure of new bio-molecules by using heavy atom derivatization (Hg, lanthanides etc.) (isomorphous replacement)

  • Fibre diffraction of bio-fibres (amyloids).

  • Difficult small molecule structure, source is Cu Kα


  • X-Ray diffraction

  • Automated crystallization set up facility

  • Automate crystal visualization camera


  • Crystal structure determination of proteins and their complexes by molecular replacement method

  • Crystal structure determination of proteins by heavy atom isomorphous replacement

Facility in-charge

Contact Email

protxrd[at] iitb[dot] ac[dot] in


Room No. 103, Ground floor, 
Sophisticated Analytical Instrument Facility (S.A.I.F),
I.I.T. Bombay, Powai, 
Mumbai - 400 076.

Contact Person:

Prof. Ruchi Anand
Prof. Prasenjit Bhaumik

Registration Link:

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Technical Specifications

Diffractometer : 

  • Maximum rated output : 1.2 kW
  • Rated tube voltage-current : 40kV; 30mA
  • Target : Cu
  • Radiation enclosure : Full safety shielding with plastic shield
  • Scanning mode : 0 - 180o ω scan: 0-180 θ scan
  • Optics : Multilayer confocal type
  • Detector : Rigaku R Axis IV ++
  • Beam size at the sample : 100 µm
  • X-Ray diffraction
  • Automated crystallization set up facility
  • Automate crystal visualization camera


In the present world of science, X-ray crystallography is the most widely used technique for determination of structures of biological macromolecules. This technique allows us to determine macromolecule structures that provides a detailed understanding of the interactions occurring at the molecular levels. Structure based drug design, study of protein-ligand interactions and structure-function relationships are the major fields where X-ray crystallography acts as a major tool. X-Ray crystallography is an experimental technique that exploits the fact that X-rays are diffracted by crystals as they have a wavelength (in Å ~10-10 m) corresponding to the size of an atom

Principle of X-ray diffraction

Each crystal has its unit cell parameters (a,b,c and α, β, γ) and in a crystal lattice infinite sets of plane can be drawn from the lattice points. These planes can be considered as source of diffraction and designated by set of miller indices. According to Braggs laws, when a wavelength (λ nm) with an angle θ passes through a crystal (which has a set of equivalent planes with hkl) a diffracted beam with the same angle is produced from which we can calculate the d spacing of the planes.

Bragg's law

                nλ = 2dsinθ

                Where    n : Order of diffracted beam
                              d : Spacing between two adjacent planes of atoms
                              λ : Wavelength of incident X-ray
                              θ : Angle of incidence of X-ray

The sets of d and intensities from protein crystals come in a unique diffraction pattern. 

Central facility presentation
Presented Date Presentation File Presentation by (Prof.) Department
04-12-2017 View Presentation1.88 MB Prof. Ruchi Anand Chemistry
08-10-2015 View Presentation2.4 MB Prof. Ruchi Anand Chemistry
28-02-2019 View Presentation3.1 MB Prof. Prasenjit Bhaumik Biosciences and Bioengineering
Publications using data from this facility

List of publications using data from the Protein Crystallography facility (2016-2022)

  • 2022:
  1. Singh, J.; Sahil, M.; Ray, S.; Dcosta, C.; Panjikar, S.; Krishnamoorthy, G.; Mondal, J.; Anand, R. Phenol Sensing in Nature Is Modulated via a Conformational Switch Governed by Dynamic Allostery. Journal of Biological Chemistry 2022298 (10), 102399.
  2. Sharma, N.; Singh, S.; Tanwar, A. S.; Mondal, J.; Anand, R. Mechanism of Coordinated Gating and Signal Transduction in Purine Biosynthetic Enzyme Formylglycinamidine Synthetase. ACS Catalysis 202212 (3), 1930–1944.
  3. Kesari, P.; Deshmukh, A.; Pahelkar, N.; Suryawanshi, A. B.; Rathore, I.; Mishra, V.; Dupuis, J. H.; Xiao, H.; Gustchina, A.; Abendroth, J.; Labaied, M.; Yada, R. Y.; Wlodawer, A.; Edwards, T. E.; Lorimer, D. D.; Bhaumik, P. Structures of Plasmepsin X from Plasmodium Falciparum Reveal a Novel Inactivation Mechanism of the Zymogen and Molecular Basis for Binding of Inhibitors in Mature Enzyme. Protein Science 202231 (4), 882–899.
  4. Sakunthala, A.; Datta, D.; Navalkar, A.; Gadhe, L.; Kadu, P.; Patel, K.; Mehra, S.; Kumar, R.; Chatterjee, D.; Devi, J.; Sengupta, K.; Padinhateeri, R.; Maji, S. K. Direct Demonstration of Seed Size-Dependent α-Synuclein Amyloid Amplification. The Journal of Physical Chemistry Letters 202213 (28), 6427–6438.
  5. Kadu, P.; Gadhe, L.; Navalkar, A.; Patel, K.; Kumar, R.; Sastry, M.; Maji, S. K. Charge and Hydrophobicity of Amyloidogenic Protein/Peptide Templates Regulate the Growth and Morphology of Gold Nanoparticles. Nanoscale 202214 (40), 15021–15033.
  6. Mehra, S.; Ahlawat, S.; Kumar, H.; Datta, D.; Navalkar, A.; Singh, N.; Patel, K.; Gadhe, L.; Kadu, P.; Kumar, R.; Jha, N. N.; Sakunthala, A.; Sawner, A. S.; Padinhateeri, R.; Udgaonkar, J. B.; Agarwal, V.; Maji, S. K. α-Synuclein Aggregation Intermediates Form Fibril Polymorphs with Distinct Prion-like Properties. Journal of Molecular Biology 2022434 (19), 167761.
  7. Chatterjee, D.; Jacob, R. S.; Ray, S.; Navalkar, A.; Singh, N.; Sengupta, S.; Gadhe, L.; Kadu, P.; Datta, D.; Paul, A.; Arunima, S.; Mehra, S.; Pindi, C.; Kumar, S.; Singru, P.; Senapati, S.; Maji, S. K. Co-Aggregation and Secondary Nucleation in the Life Cycle of Human Prolactin/Galanin Functional Amyloids. eLife 202211.

  • 2021:
  1. Godsora, B. K. J.; Prakash, P.; Punekar, N. S.; Bhaumik, P. Molecular Insights into the Inhibition of Glutamate Dehydrogenase by the Dicarboxylic Acid Metabolites. Proteins: Structure, Function, and Bioinformatics 202190 (3), 810–823.

  • 2020:
  1. Sharma, N.; Ahalawat, N.; Sandhu, P.; Strauss, E.; Mondal, J.; Anand, R. Role of Allosteric Switches and Adaptor Domains in Long-Distance Cross-Talk and Transient Tunnel Formation. Science Advances 20206 (14).
  2. Rathore, I.; Mishra, V.; Patel, C.; Xiao, H.; Gustchina, A.; Wlodawer, A.; Yada, R. Y.; Bhaumik, P. Activation Mechanism of Plasmepsins, Pepsin‐like Aspartic Proteases from Plasmodium, Follows a Unique Trans‐Activation Pathway. The FEBS Journal 2020288 (2), 678–698.
  3. Badgujar, D. C.; Anil, A.; Green, A. E.; Surve, M. V.; Madhavan, S.; Beckett, A.; Prior, I. A.; Godsora, B. K.; Patil, S. B.; More, P. K.; Sarkar, S. G.; Mitchell, A.; Banerjee, R.; Phale, P. S.; Mitchell, T. J.; Neill, D. R.; Bhaumik, P.; Banerjee, A. Structural Insights into Loss of Function of a Pore Forming Toxin and Its Role in Pneumococcal Adaptation to an Intracellular Lifestyle. PLOS Pathogens 2020, 16 (11), e1009016.
  4. Kadu, P.; Pandey, S.; Neekhra, S.; Kumar, R.; Gadhe, L.; Srivastava, R.; Sastry, M.; Maji, S. K. Machine-Free Polymerase Chain Reaction with Triangular Gold and Silver Nanoparticles. The Journal of Physical Chemistry Letters 202011 (24), 10489–10496.

  • 2019:
  1. Yarramala, D. S.; Prakash, P.; Ranade, D. S.; Doshi, S.; Kulkarni, P. P.; Bhaumik, P.; Rao, C. P. Cytotoxicity of Apo Bovine α-Lactalbumin Complexed with La 3+ on Cancer Cells Supported by Its High Resolution Crystal Structure. Scientific Reports 20199 (1), 1780.

  • 2018:
  1. Pandey, S.; Phale, P. S.; Bhaumik, P. Structural Modulation of a Periplasmic Sugar-Binding Protein Probes into Its Evolutionary Ancestry. Journal of Structural Biology 2018204 (3), 498–506.
  2. Mishra, V.; Rathore, I.; Arekar, A.; Sthanam, L. K.; Xiao, H.; Kiso, Y.; Sen, S.; Patankar, S.; Gustchina, A.; Hidaka, K.; Wlodawer, A.; Yada, R. Y.; Bhaumik, P. Deciphering the Mechanism of Potent Peptidomimetic Inhibitors Targeting Plasmepsins – Biochemical and Structural Insights. The FEBS Journal 2018285 (16), 3077–3096.
  3. Wangchuk, J.; Prakash, P.; Bhaumik, P.; Kondabagil, K. Bacteriophage N4 Large Terminase: Expression, Purification and X-Ray Crystallographic Analysis. Acta Crystallographica Section F Structural Biology Communications 201874 (4), 198–204.
  4. Prakash, P.; Punekar, N.; Bhaumik, P. Structural Basis for the Catalytic Mechanism and α-Ketoglutarate Cooperativity of Glutamate Dehydrogenase. Journal of Biological Chemistry 2018, 293(17), 6241-6258.
  5. Kirti, S.; Patel, K.; Das, S.; Shrimali, P.; Samanta, S.; Kumar, R.; Chatterjee, D.; Ghosh, D.; Kumar, A.; Tayalia, P.; Maji, S. K. Amyloid Fibrils with Positive Charge Enhance Retroviral Transduction in Mammalian Cells. ACS Biomaterials Science & Engineering 20185 (1), 126–138.
  6. Mehra, S.; Ghosh, D.; Kumar, R.; Mondal, M.; Gadhe, L. G.; Das, S.; Anoop, A.; Jha, N. N.; Jacob, R. S.; Chatterjee, D.; Ray, S.; Singh, N.; Kumar, A.; Maji, S. K. Glycosaminoglycans Have Variable Effects on α-Synuclein Aggregation and Differentially Affect the Activities of the Resulting Amyloid Fibrils. Journal of Biological Chemistry 2018293 (34), 12975–12991.
  7. Sharma, H.; John, K.; Gaddam, A.; Navalkar, A.; Maji, S. K.; Agrawal, A. A Magnet-Actuated Biomimetic Device for Isolating Biological Entities in Microwells. Scientific Reports 20188 (1).

  • 2017:
  1. Gaded, V.; Anand, R. Selective Deamination of Mutagens by a Mycobacterial Enzyme. Journal of the American Chemical Society 2017139 (31), 10762–10768.
  2. Ray, S.; Maitra, A.; Biswas, A.; Panjikar, S.; Mondal, J.; Anand R. Functional Insights into the Mode of DNA and Ligand Binding of the Tetr Family Regulator Tylp from Streptomyces fradiae.  Journal of Biological Chemistry 2017292 (37), 15301-15311.
  3. Ghosh, S.; Salot, S.; Sengupta, S.; Navalkar, A.; Ghosh, D.; Jacob, R.; Das, S.; Kumar, R.; Jha, N. N.; Sahay, S.; Mehra, S.; Mohite, G. M.; Ghosh, S. K.; Kombrabail, M.; Krishnamoorthy, G.; Chaudhari, P.; Maji, S. K. P53 Amyloid Formation Leading to Its Loss of Function: Implications in Cancer Pathogenesis. Cell Death & Differentiation 201724 (10), 1784–1798.

  • 2016:
  1. Pandey, S.; Modak, A.; Phale, P. S.; Bhaumik, P. High Resolution Structures of Periplasmic Glucose-Binding Protein of Pseudomonas Putida CSV86 Reveal Structural Basis of Its Substrate Specificity. Journal of Biological Chemistry 2016291 (15), 7844–7857.
  2. Jacob, R. S.; Das, S.; Ghosh, S.; Anoop, A.; Jha, N. N.; Khan, T.; Singru, P.; Kumar, A.; Maji, S. K. Amyloid Formation of Growth Hormone in Presence of Zinc: Relevance to Its Storage in Secretory Granules. Scientific Reports 20166 (1).
  3. Jacob, R. S.; George, E.; Singh, P. K.; Salot, S.; Anoop, A.; Jha, N. N.; Sen, S.; Maji, S. K. Cell Adhesion on Amyloid Fibrils Lacking Integrin Recognition Motif. Journal of Biological Chemistry 2016291 (10), 5278–5298.
Instructions for sample preparation/submission
  • Well isolated protein crystals obtained via sitting/hanging drop method.
  • Crystals flash frozen in liquid nitrogen using appropriate cryo-protectant and maintained in a Dewar can also be provided.
  • The user has to come with prepared Cryo-protectant solutions.
  • Coverslips, bridges for soaking and loops appropriate for your proteins will be provided only on request.
Instructions for Users
  • At the time of X-ray diffraction of crystal, the user should be present.
  • Images of diffraction will be given in CD format. Please bring your own CD. USB drives are strictly not allowed due to virus threat.
  • Samples and Measurement data should be collected as soon as the diffraction gets completed with a maximum duration of one week.
Instructions for Registration

Only online registration through the IRCC webpage will be accepted. The users will be informed about their date and time of slot by email. If the appointment is given but the user cannot come, a mail should be immediately sent to protxrd [at] iitb [dot] ac [dot] in to cancel his/her slot.