X-ray crystallography and structure elucidation MCQs With Answer

X-ray crystallography is a core technique for structure elucidation in pharmaceutical research, enabling determination of atomic arrangements in small molecules and macromolecules. For B. Pharm students, mastering concepts such as Bragg’s law, unit cell parameters, space groups, reciprocal lattice, electron density maps and refinement is essential to interpret molecular geometry, stereochemistry and ligand–receptor interactions. Practical aspects include crystal growth, data collection, detector types, resolution limits, phase determination (Patterson, direct methods, SAD/MAD), and model validation (R-factor, B‑factors). This concise review emphasises both theory and practical workflows to prepare you for analysis and reporting of crystal structures in drug development. Now let’s test your knowledge with 30 MCQs on this topic.

Q1. What fundamental equation relates X-ray wavelength, interplanar spacing and diffraction angle in crystallography?

• Bragg’s law (nλ = 2d sinθ)
• Snell’s law (n1 sinθ1 = n2 sinθ2)
• de Broglie equation (λ = h/p)
• Beer–Lambert law (A = εcl)

Correct Answer: Bragg’s law (nλ = 2d sinθ)

Q2. Which definition best describes the crystallographic unit cell?

• The smallest repeating volume that builds the entire crystal lattice
• A single molecule isolated from the crystal
• The region of highest electron density only
• The detector area used in diffraction experiments

Correct Answer: The smallest repeating volume that builds the entire crystal lattice

Q3. Which space group is the simplest and contains only the identity operation?

• P1 (space group 1)
• P2₁ (space group 4)
• Pm (space group 6)
• P2/m (space group 10)

Correct Answer: P1 (space group 1)

Q4. The reciprocal lattice in X-ray crystallography corresponds to which of the following?

• The Fourier transform of the real (direct) lattice producing diffraction points
• A physical lattice inside the crystal visible under microscope
• A model of atomic vibrations at high temperature
• The chemical bonding network in the molecule

Correct Answer: The Fourier transform of the real (direct) lattice producing diffraction points

Q5. What is the crystallographic “phase problem”?

• Diffraction experiments measure intensities but not phases of structure factors
• Determining the absolute configuration of a chiral center from X-rays
• Loss of crystal order due to radiation damage
• Ambiguity in unit cell determination from powder data

Correct Answer: Diffraction experiments measure intensities but not phases of structure factors

Q6. Which method is commonly used to locate heavy atoms in an unknown structure early in solving phases?

• Patterson map analysis
• Fourier transform of the final model
• Direct hydrogen placement
• Rietveld refinement

Correct Answer: Patterson map analysis

Q7. Direct methods for phase determination are most effective for which class of samples?

• Small-molecule crystals with high-resolution data (~1.2 Å or better)
• Large protein crystals (>50 kDa)
• Amorphous solids without long-range order
• Powder samples with overlapping peaks

Correct Answer: Small-molecule crystals with high-resolution data (~1.2 Å or better)

Q8. Which experimental phasing technique exploits differences in scattering at different wavelengths?

• MAD/SAD (multi-wavelength or single-wavelength anomalous dispersion)
• Isomorphous replacement without heavy atoms
• Direct methods using electron density
• Rietveld method for powder diffraction

Correct Answer: MAD/SAD (multi-wavelength or single-wavelength anomalous dispersion)

Q9. In crystallographic refinement, what does the R-factor measure?

• The agreement between observed and calculated structure factor amplitudes
• The strength of chemical bonds in the model
• The resolution of the diffraction data in Ångström
• The crystal mosaic spread

Correct Answer: The agreement between observed and calculated structure factor amplitudes

Q10. What does a reported resolution of 1.8 Å for a crystal structure indicate?

• Reflections were measured down to a minimum d-spacing of 1.8 Å
• The unit cell edges measure 1.8 Å each
• The R-factor is 1.8%
• The crystal mosaicity equals 1.8 degrees

Correct Answer: Reflections were measured down to a minimum d-spacing of 1.8 Å

Q11. What does the atomic B-factor (temperature factor) describe?

• The amplitude of atomic thermal motion or static disorder
• The oxidation state of a metal ion
• The binding affinity of a ligand
• The pH at which the crystal was grown

Correct Answer: The amplitude of atomic thermal motion or static disorder

Q12. Twinning in crystals results in which complication during data processing?

• Overlapping diffraction patterns from multiple domain orientations
• Complete absence of diffraction peaks
• Excessive anomalous signal at all wavelengths
• Automatic solution of phases without refinement

Correct Answer: Overlapping diffraction patterns from multiple domain orientations

Q13. Which crystal system is consistent with unit cell angles α = β = 90°, γ = 120°?

• Hexagonal
• Orthorhombic
• Monoclinic
• Triclinic

Correct Answer: Hexagonal

Q14. A chiral molecule must crystallize in which type of space groups to preserve absolute chirality?

• Chiral space groups lacking mirror, glide, inversion or roto-inversion symmetry
• Any centrosymmetric space group
• Only cubic space groups
• Only space groups with mirror planes

Correct Answer: Chiral space groups lacking mirror, glide, inversion or roto-inversion symmetry

Q15. Compared with in-house X-ray sources, synchrotron radiation provides what main advantages?

• Much higher intensity and tunable wavelength for rapid, high-resolution data
• Lower intensity but simpler data processing
• Only useful for powder diffraction
• Generates visible light instead of X-rays

Correct Answer: Much higher intensity and tunable wavelength for rapid, high-resolution data

Q16. Which detector type is commonly used for modern single-crystal data collection?

• Area detectors such as CCD or hybrid pixel detectors
• Photographic film only
• Pearson spectrometer
• Mass spectrometer

Correct Answer: Area detectors such as CCD or hybrid pixel detectors

Q17. Why is absorption correction applied to diffraction intensities?

• To correct for X-ray attenuation within the crystal and improve intensity accuracy
• To remove background scattering from the detector
• To calculate atomic occupancies directly
• To convert intensities to wavelengths

Correct Answer: To correct for X-ray attenuation within the crystal and improve intensity accuracy

Q18. Systematic absences in diffraction data help identify which symmetry elements?

• Screw axes and glide planes
• Isotropic displacement parameters
• Solvent content
• Hydrogen atom positions

Correct Answer: Screw axes and glide planes

Q19. Which statement correctly contrasts powder diffraction with single-crystal diffraction?

• Powder diffraction yields 1D patterns from many randomly oriented crystallites, making 3D structure solution more challenging
• Powder diffraction directly gives phases without models
• Single-crystal diffraction cannot provide atomic coordinates
• Powder diffraction always gives higher resolution than single-crystal methods

Correct Answer: Powder diffraction yields 1D patterns from many randomly oriented crystallites, making 3D structure solution more challenging

Q20. An electron density map is obtained by which mathematical operation on structure factors?

• Inverse Fourier transform of structure factors (Fobs with phases)
• Direct differentiation of intensities with respect to angle
• Multiplication of all observed amplitudes
• Integration of the unit cell volume only

Correct Answer: Inverse Fourier transform of structure factors (Fobs with phases)

Q21. Crystallographic refinement typically minimizes which target function?

• The least-squares difference between observed and calculated structure factors
• The unit cell volume
• The number of atoms in the asymmetric unit
• The wavelength of the X-rays

Correct Answer: The least-squares difference between observed and calculated structure factors

Q22. The B-factor can also be reported as which alternative term?

• Temperature factor
• Bond order
• Occupancy parameter
• Resolution shell

Correct Answer: Temperature factor

Q23. What is the purpose of reporting Rfree in macromolecular refinement?

• Cross-validation using a subset of reflections not used in refinement
• Measuring the crystal’s physical weight
• Quantifying solvent content only
• Defining unit cell symmetry

Correct Answer: Cross-validation using a subset of reflections not used in refinement

Q24. Isomorphous replacement requires which strategy to obtain phase information?

• Comparing native and heavy-atom derivative intensities to determine phase differences
• Collecting data at cryogenic temperatures only
• Using only direct methods without heavy atoms
• Refining B-factors without coordinates

Correct Answer: Comparing native and heavy-atom derivative intensities to determine phase differences

Q25. Laue diffraction uses what kind of X-ray beam compared to standard rotation methods?

• Polychromatic (white) beam instead of monochromatic radiation
• Only visible light
• Monochromatic beam with fixed wavelength
• Neutron beam exclusively

Correct Answer: Polychromatic (white) beam instead of monochromatic radiation

Q26. What does crystal mosaicity describe?

• The spread of orientations of small crystalline domains within a crystal
• The chemical heterogeneity of the molecule
• The number of atoms per asymmetric unit
• The percentage of solvent in the unit cell

Correct Answer: The spread of orientations of small crystalline domains within a crystal

Q27. An atomic occupancy value less than 1 typically indicates what?

• Partial occupancy or disorder at that site
• The atom is heavier than expected
• The atom is fixed by symmetry
• The atom is not refined

Correct Answer: Partial occupancy or disorder at that site

Q28. Why are hydrogen atoms often difficult to locate in X-ray crystal structures?

• Hydrogen has only one electron, producing weak X-ray scattering
• Hydrogen absorbs all X-rays and prevents diffraction
• Hydrogen atoms are too large to fit in unit cells
• Hydrogen atoms change symmetry of the crystal

Correct Answer: Hydrogen has only one electron, producing weak X-ray scattering

Q29. What information does a Patterson map primarily provide?

• Vector relationships between atomic positions, useful for locating heavy atoms
• Absolute phases for all reflections directly
• The chemical formula of the compound
• The exact positions of all hydrogen atoms

Correct Answer: Vector relationships between atomic positions, useful for locating heavy atoms

Q30. What does the acronym PDB stand for in structural biology and crystallography?

• Protein Data Bank
• Primary Diffraction Baseline
• Phase Determination Browser
• Polymorph Database

Correct Answer: Protein Data Bank

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