Institute of Crystallography - CNR

Carrozzini Benedetta


Dr. Benedetta Carrozzini received her M.Sc. degree in Geological Sciences (with honors) at Bari University in 1987 and she got a PhD diploma in Earth Sciences at the same University in 1992. From 1993 to 2000 he was postdoctoral researcher and visiting scientist at the Institute for Crystallographic Methodologies Development (IRMEC) of the National Research Council (CNR), supervisor Prof. C. Giacovazzo. Since February 2001, she has a permanent position as staff researcher at the Institute of Crystallography (CNR) in Bari.

Since 2009 she is the Unit Leader for the CNR research activity devoted to the “Development and application of crystallographic methods for structure determination of molecules, with different nature and complexity, by single crystal (X-rays and electron) diffraction data”.

She is author of crystallographic software packages [SIR suite (vers.1999-2019), Il Milione (vers. 2007), EXPO (vers. 1999)], widely used in scientific labs around the world.

She was involved in several research projects (some currently in progress) and she was Work-TaskLeader for H2020 FET-OPEN AMECRYS Project (2016/2021). In 2016 she was a visiting scientist at the KNU Creative BioResearch Group (Prof. E. di Luccio), in Daegu (South Korea).

In 2008-2011 she was Effective Member of the IUCr Crystallographic Computing Commission, and then Consultant in the following three years.

She is author of over 85 papers in international peer-reviewed journals (Scopus H-index = 21).

She presented several communications at (national and international) meetings and workshops and lectures at international training schools; in many cases she served on their respective scientific and organizing committees.

(detailed list of publications:

Dr. Carrozzini’s research activity is mainly addressed to:

– development of innovative methodologies aimed at improving the structure determination process of crystal molecules with different chemical composition and structural complexity (i.e. small organic or inorganic compounds up to nucleic acids and proteins),

– implementation of the new theories, algorithms and computing tools in powerful crystallographic software, devoted to the automatic structure solution via single crystal data, using X-ray or electron diffraction patterns.

Single crystal data analysis for the structure characterization of small compounds and macromolecules.

The main research interests and skills concern: Ab initio phasing approaches (Direct Methods, Patterson Deconvolution techniques), Molecular Replacement, Electron Density Modification (EDM/DEDM) techniques, structure refinement (Fourier analysis), Automated Model Building, X-ray or electron Diffraction, Protein Crystallography.

Università di Perugia – Dipart. di Fisica e Geologia

Università di Bari: Dipart. di Chimica, Scienze del Farmaco, Bioscienze, Biotecnologie e Biofarmaceutica,



CNR- FOCUS 2007: New record in the ab-initio structural solution of proteins (01/01/2007)
While the phase problem in crystallography is definitively solved for small molecules, it is still a challenge for macromolecular crystallography. This is one of the most challenging areas of Modern Sciences and constitutes the primary tool for structural studies on complex biological systems, and for explaining the mechanisms underlying life. In fact, macromolecular crystallography allows to determine the crystalline structure of proteins, nucleic acids, viruses, etc. and provides details for understanding a wide variety of life processes, such as photosynthesis, transmission of hereditary information, viral infections, etc. Crystallographic methods for the solution of crystalline structures are of primary importance for macromolecular crystallography: their effectiveness is responsible for the success or failure of the research and governs the economic aspects of the activities (innovation in methods can accelerate research, allows to save man-months and resources, improve the quality of results, facilitate the creation of research groups and scientific services). Generally molecular complexity and  low resolution of the experimental pattern make the data of  native protein alone insufficient for structure solution. Therefore, in addition to ab-initio techniques, those called SIR (Single Isomorphous Replacement), MIR (Multiple Isomorphous Replacement), SAS (Single Anomalous Scattering), MIRAS (combination of MIR techniques with anomalous diffusion effects), MAD (Multiple Anomalous Dispersion) and MR (Molecular Replacement) constitute the body of the methods currently used to determine macromolecular structures. The research developed by the IC researchers  made a significant contribution in many of the above mentioned fields. In particular: a) Ab-Initio techniques have been developed to push the limits of atomic resolution up to 2.0 Å, extending widely the number of structures that can be treated by these techniques; b) algorithms have been introduced for the extrapolation of unmeasured reflections (Free-Lunch) for structures with non-atomic resolution. They are able to favor the solution and improve the quality of electron density maps; c) the SIR-MIR-SIRAS-MIRAS-SAD-MAD techniques were integrated with Direct Methods, making the latter suitable for the treatment of errors, both those coming from the experiments, and those related to the structural model or loss of isomorphism. The joint probability distribution functions method was the mathematical tool used to derive new formulas. New probabilistic theories and new algorithms have been implemented in a package for the automatic solution of the phase problem for macromolecules, called Il Milione (1). The application to hundreds of protein test structures shows the high efficiency of this approach, its validity in the face of experimental errors, its ability to automatically provide a correct structure model of the protein, with virtually no user intervention. Until 2006, the largest protein solved by Ab-Initio techniques was cytochrome C3 (Sheldrick 1998, 218 residues). This limit was exceeded in 2006 by Mooers & Matthews who, using Sir2002, resolved the structure of bacteriophage P22 lysozyme (292 residues). Subsequently, the IC software was able to extend the structural complexity of the Ab-Initio solvable proteins, bringing the limit to 748 residues. In recent days, the record of the largest protein solved by Ab-Initio techniques has been exceeded, however, held by the programs developed by the IC researchers, reaching the limit of 984 residues. The protein, 1.65Å resolution, PDB code 1E3U, was automatically solved in 80 minutes. Il Milione is a valuable tool for the development of genomics and post-genomics and is available to the scientific community. The software can be downloaded from the Institute of Crystallography website (
(1) M.C. Burla, R. Caliandro, M. Camalli, B. Carrozzini, G.L. Cascarano, L. De Caro, C. Giacovazzo, G. Polidori, D. Siliqi, R. Spain (2007). THE MILLION: a suite of computer programs for crystal structure solution of proteins – J. Appl. Cryst. 40, 609-613

ANKA HIGHLIGHTS (2013/14): Unravelling Cobalt Binding to Photosynthetic Bacterium by X-ray Absorption Spectroscopy (14/05/2015)

X-ray absorption spectroscopy was used to characterize the fate of cobalt ions present in the growth media of the photosynthetic bacterium Rhodobacter sphaeroides, a microorganism with high metal tolerance and considered a potential target for bioremediation processes.

Results show that, in the average, cobalt binds in whole cells mostly to carboxylate moieties, with a very small contribution of sulfoxide or sulfonate moiety. A detailed analysis shows that this contribution arises from the sole cell envelope, where the sulphur appear to be as important as carbon in the second coordination shell of cobalt, indicating that sulfolipids of the photosynthetic membrane can significantly contribute to cobalt binding in Rhodobacter sphaeroides [1].

[1] Cobalt binding in the photosynthetic bacterium R. sphaeroides by X-ray absorption spectroscopy. B.D. Belviso, F. Italiano, R. Caliandro, B. Carrozzini, A. Costanza, M. Trotta. (2013) BioMetals 26(5): 693-703. DOI: 10.1007/s10534-013-9641-3.

Publisher: Karlsruhe Institute of Technology (KIT); ANKA – Synchrotron Radiation Facility

CNR – NEWS (2016): Membrane crystallization: new method of industrial production of monoclonal antibodies (08/03/2016)

The AMECRYS project (Revolutionizing Downstream Processing of Monoclonal Antibodies by Continuous Template-Assisted Membrane Crystallization), coordinated by the CNR, has just been admitted for funding under the “Future Emerging Technologies” call for the Horizon2020 program (call H2020-FETOPEN-2014 / 2015). It was selected from among the 800 eligible projects presented in the RIA section, scoring the maximum score in all areas of evaluation: excellence, impact, quality and efficiency of implementation. It provides for a 4-year loan, for a total of 3.5 million euros, and will be led by a team made up of two research institutions: CNR and CNRS in France; four Universities: University of Calabria, Imperial College of London, Strathclyde University of Glasgow, Free University of Brussels; three companies: Center for Processing Innovation (UK), GVS Filter Technology S.p.a., one of the world’s largest producers of membranes and filters, Fujifilm Diosynth Biotechnologies, a supplier of biological macromolecules and services for biopharmaceutical companies. The CNR is present with three Institutes: the Institute for Membrane Technology (CNR-ITM) in Rende (Cs), the Institute of Crystallography (CNR-IC) in Bari and the Institute for the Applications of Computing (CNR -IAC) in Bari. The project idea, extremely innovative and ambitious, comes from a multi-year collaboration between the group of Dr. Gianluca Di Profio (CNR-ITM) and that of Dr. Rocco Caliandro (CNR-IC), which led to the publication of numerous articles that have appeared in high-impact journals such as Crystal Growth & Design, Advanced Functional Materials and Advanced Materials. It aims to revolutionize the current industrial production processes of monoclonal antibodies (mAbs) by creating continuously operating membrane crystallizers, capable of to separate and purify biological macromolecules directly from their culture broth. This will save approximately 60% of the current mAbs production costs. The crystallization of mAbs directly from a multi-component solution has never been realized so far, and represents the most ambitious challenge that the researchers will face during the project, starting from three strengths: the efficiency of crystallization technology based on engineered membrane technology, the capacity to induce selective crystallization using appropriately functionalized nanomaterials, the “pharma-on-a-chip” approach using microfluidic devices specially designed for continuous flow crystallization. This strategy will be supported by a detailed analysis of the properties of the crystals produced and by an intense computational effort, aimed at investigating the molecular mechanisms underlying the crystallization process, and to study the relationship between the multiple experimental variables and the results of crystallization.

CNR – NEWS (2019): Discovery of a new protein involved in the epigenetic mechanisms underlying male infertility (28/02/2019)

The Set7 protein, produced by the organism Schizosaccharomyces pombe and belonging to the histone-methyltransferase (HMT) family, was identified and characterized. HMTs are involved in the histone methylation mechanism, so they play a key role in the transcriptional regulation process. The study of the interactions between HMT and their different substrates is therefore of extreme importance for the understanding of the mechanisms that regulate gametogenesis and / or spermatogenesis. The research stems from the collaboration between the Institute of Crystallography (CNR-IC) in Bari [Dr. Caliandro’s group] and the Kyungpook National University in Daegu (South Korea) [Dr. di Luccio’s group], established as a result of a bilateral project funded by CNR and Korean National Research Foundation, and was published by the prestigious international journal Structure (CellPress). Set7 shows a unique amino acid sequence among the known HMTs (the closest homologue has a sequence identity of 23%), so the determination of its atomic structure (shown in the figure) by means of X-ray diffraction was only possible thanks to the use of latest generation algorithms, analyzed by SIR2014 computing program developed and distributed by the CNR-IC researchers. Set7 in crystalline form appears as a homo-dimer, a rather rare configuration for this type of protein. The research led to the clarification of the methylation mechanism and the role of the Set7 protein in the epigenetic regulation of S. pombe gametogenesis. It was shown that methylation levels increase dramatically during gametogenesis and that Set7 deletion mutant cells show defects and produce an excessive number of spores with abnormal morphology. These results support the link between the Set7 protein, the H3K37 epigenetic mark and correct gametogenesis in S. pombe. Since S. pombe gametogenesis shows similarities to mammalian spermatogenesis, this study paves the way for a better understanding of the mechanisms underlying human male infertility.

CNR-IC research selected for publication in Special Collection “AlphaFold: Applicationsof 3D Protein Structure in Diagnosis and Therapeutics” (10/11/2022)
The article “Structural Characterization of the Full-Length Anti-CD20 Antibody Rituximab”, published in the journal “Frontiers in Molecular Biosciences” by the researchers of the IC-CNR B.D. Belviso, G.F. Mangiatordi, V. Mangini, B. Carrozzini and R. Caliandro, in collaboration with CINECA colleague D. Alberga, was selected to be included in the Special Collection “AlphaFold: Applications of 3D Protein Structure in Diagnosis and Therapeutics”. The Editors of the journal motivated this choice for the relevance of the topic addressed and for the quality of the results obtained, thus rewarding the working group for the interesting research aimed at characterizing the overall structure of the Rituximab antibody, in solution, by SAXS data analysis. This molecule is the first monoclonal antibody (mAb) specially developed as a therapeutic agent against the CD20 protein, responsible for numerous autoimmune diseases, various forms of leukemia and lymphomas. The results obtained may be useful to facilitate the design of new generation anti-CD20 antibodies and to identify more efficient industrial production processes of Rituximab.
The Automatic Solution of Macromolecular Crystal Structures via Molecular Replacement Techniques: REMO22 and Its Pipeline

Carrozzini, Benedetta; Cascarano, Giovanni Luca; Giacovazzo, Carmelo

International journal of molecular sciences (Online) (2023)

Extending Ab Initio Phasing up to 2.2 Å Resolution: New Superposition Techniques

Maria Cristina Burla, Benedetta Carrozzini, Giovanni Luca Cascarano, Carmelo Giacovazzo, Giampiero Polidori

Crystals (Basel) (2023)

Structural Characterization of the Full-Length Anti-CD20 Antibody Rituximab

Belviso B.D.; Mangiatordi G.F.; Alberga D.; Mangini V.; Carrozzini B.; Caliandro R.

Frontiers in Molecular Biosciences (2022)

Enantiomeric Separation and Molecular Modelling of Bioactive 4-Aryl-3,4-dihydropyrimidin-2(1H)-one Ester Derivatives on Teicoplanin-Based Chiral Stationary Phase

Bolognino, Isabella; Carrieri, Antonio; Purgatorio, Rosa; Catto, Marco; Caliandro, Rocco; Carrozzini, Benedetta; Belviso, Benny Danilo; Majellaro, Maria; Sotelo, Eddy; Cellamare, Saverio; Altomare, Cosimo Damiano

Separations (2022)

Deep Eutectic Solvents A new opportunity for protein crystallization

Benny Danilo Belviso, Filippo Maria Perna, Benedetta Carrozzini, Massimo Trotta, Vito Capriati, Rocco Caliandro


Introducing Protein Crystallization in Hydrated Deep Eutectic Solvents

Benny Danilo Belviso, Filippo Maria Perna, Benedetta Carrozzini, Massimo Trotta,* Vito Capriati,* and Rocco Caliandro

ACS sustainable chemistry & engineering (2021)