CHEM 3453, Homework 6 Student Name:

30 Points
Due Date: 4/4/2021

Problem 6.1 (9 Points. Tinoco 15.16). An x-ray beam of wavelength 0.154 nm shines on a crystal.

a. Two beams scattered from the crystal are exactly out of phase at the detector, what would be three
possible values for the path differences in angstroms?

For the beams to be out-of-phase, the smallest path differences would be

1 1
λ= ∗ 0.154 = 0.077 nm
2 2
3 3
λ= ∗ 0.154 = 0.231 nm
2 2
5 5
λ= ∗ 0.154 = 0.385 nm
2 2

b. A Bragg reflection occurs in the first order at 5.00◦ . What is the distance in angstroms between the
scattering planes causing this reflection?

The Bragg’s equation is

nλ = 2d sinθ

For a first-order reflection, n = 1. Therefore,

nλ 1 ∗ 0.154
d= = = 0.883 nm
2 sinθ 2 ∗ sin(5◦ )

c. What is the smallest value of distance between two scattering planes that can be detected with this
0.154 nm x-ray?

With
nλ
d= ,
2 sinθ
the smallest distance at occurs at n = 1 and θ = 90◦ ,
nλ 1∗λ 1
d= = ◦
= λ = 0.077 nm
2 sinθ 2 sin(90 ) 2

1
Problem 6.2 (6 Points. Atkins 11.24).

a. Calculate the separations of the planes (111), (211), and (100) in a crystal in which the cubic unit cell
has sides of length 532 pm.
For a cubic lattice,
− 12
h2 k 2 l2

a
dhkl = + + =√
a2 b2 c2 h2 + k 2 + l2
Therefore
a a a 532
d111 = √ =√ = √ = √ = 307.2 pm
h2 + k 2 + l2 12 + 1 2 + 1 2 3 3
a a a 532
d211 =√ =√ = √ = √ = 217.2 pm
h2 + k 2 + l2 22 + 1 2 + 1 2 6 6
a a a 532
d100 =√ =√ = √ = √ = 532.0 pm
h2 + k 2 + l2 12 + 0 2 + 0 2 1 1

b. Calculate the separations of the planes (123) and (236) in an orthorhombic crystal in which the unit
cell has sides of lengths 0.754, 0.623, and 0.433 nm.
For an orthorhombic lattice,
− 21
h2 k 2 l2

dhkl = + +
a2 b2 c2

Therefore,
− 12
12 22 32

d123 = + + = 0.1290 nm
0.7542 0.6232 0.4332
− 12
22 32 62

d236 = + + = 0.0671 nm
0.7542 0.6232 0.4332

Problem 6.3 (5 Points. Atkins 11.25). The glancing angle of a Bragg reflection from a set of crystal
planes separated by 97.3 pm is 19.85◦ . Calculate the wavelengths of the X-rays.
The Bragg’s equation is

nλ = 2d sinθ

Therefore,

λ = 2d sinθ = 2 ∗ 97.3 ∗ sin(19.85◦ ) = 66.08 pm

2
Problem 6.4 (5 Points). Find the PDB entry for 2D1R in the Protein Data Bank online (rcsb.org).
Answer the following questions from the data online about this PDB entry and its related links.

a. What is the literature citation (journal, year, volume, and starting page) that reported this crystal
structure?
The reference is ”Structural basis for the spectral difference in luciferase bioluminescence. Nakatsu,
T., Ichiyama, S., Hiratake, J., Saldanha, A., Kobashi, N., Sakata, K., Kato, H. (2006) Nature 440:
372-376.”

b. What is the resolution of these crystals?

The resolution for this crystal structure is 1.60Å.

c. What are the crystallization pH conditions for growing this crystal?

The experimental pH value is 8.0.

d. What are the unit cell dimensions? What is the shape of the unit cell?
The unit cell dimension is

Therefore, the unit cell is orthorhombic.

e. In this crystal structure, there is a ligand with two sulfur atoms. Draw its chemical structure.
The ligand structure is

with the actual chemical structure being

3
Problem 6.5 (5 Points). Find the PDB entries for 6XRA and 6XR8 in the Protein Data Bank online
(rcsb.org). Answer the following questions from the data online about these PDB entries and their related
links.

a. What is the literature citation (journal, year, volume, and starting page) that reported these struc-
tures?
The reference is “Distinct conformational states of SARS-CoV-2 spike protein. Cai, Y., Zhang, J.,
Xiao, T., Peng, H., Sterling, S.M., Walsh Jr., R.M., Rawson, S., Rits-Volloch, S., Chen, B. (2020)
Science 369: 1586-1592”.

b. What is the resolution of these structures?

The resolutions are 3.00Å (6XRA) and 2.90Å (6XR8)

c. What are the biological functions of these structures?

6XR8 is the pre-fusion conformation of the spike protein (before it binds to human ACE2 receptor),
whereas 6XRA is the post-fusion conformation.