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Structure Refinement: Completing The Structure and Evaluating How Good Your Data and Model Agree

The document discusses structure refinement in X-ray crystallography. During refinement, initial atomic positions obtained from methods like Patterson analysis are optimized to improve agreement between observed and calculated structure factors. Refinement involves iterative least-squares minimization to reduce differences between measured and calculated structure factor magnitudes. The goal is to minimize an R-factor until parameter changes are insignificant, indicating convergence on the best-fitting model. Statistical values like R-factors and goodness-of-fit are used to evaluate refinement quality.

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Maykel Manawan
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37 views

Structure Refinement: Completing The Structure and Evaluating How Good Your Data and Model Agree

The document discusses structure refinement in X-ray crystallography. During refinement, initial atomic positions obtained from methods like Patterson analysis are optimized to improve agreement between observed and calculated structure factors. Refinement involves iterative least-squares minimization to reduce differences between measured and calculated structure factor magnitudes. The goal is to minimize an R-factor until parameter changes are insignificant, indicating convergence on the best-fitting model. Statistical values like R-factors and goodness-of-fit are used to evaluate refinement quality.

Uploaded by

Maykel Manawan
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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Download as PDF, TXT or read online on Scribd
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Structure refinement

Completing the structure and evaluating how good


your data and model agree

Why you should refine a structure

We have considered how atoms are located by Patterson, direct


methods or specialized methods, as well as from Fourier
difference maps

The atomic positions extracted from these methods are close to


the correct values, but very rarely in exactly the right place

During a process called refinement, the starting atomic


positions are optimized
- the goal is to get an as good fit between your model and your data as
possible

Possible refinement methods

You can modify your model in order to obtain better


agreement between observed and calculated Fourier maps

Alternatively, you can modify your model to get better


agreement between observed and calculated structure
factor magnitudes (|Fo| and |Fc|)

For most small molecule structure solutions, the latter


process is used

Letting the computer do the work

The refinement process can be described as a minimization process


- minimization of the difference between |Fo| and |Fc|
- easily automated

The best model is obtained by minimizing the following expression:

R' = whkl ( Fo k Fc ) 2
hkl

- called a least squares minimization


- wkhl are weighing factors related to the quality/reliability of the data
- k is a scale factor (inverse of scale factor that would need to be applied to |Fo|

Least squares minimization

Imagine a function F that is linearly dependent on a set of


parameters, xj
- F(x1,x2,xn) = p1x1 + p2x2 + pnxn

Suppose we make m independent measurements of F for different


values of xj
- we want to get the parameters pj
- if m = n, we just have to solve a set of simultaneous equations
- if m > n, the system is overdetermined

Crystallography and least squares

The crystallographic function F(hkl) (with the variables: atomic


coordinates and thermal parameters of each atom) is not a linear
function of the model parameters
N

F(hkl) = f j exp[2i (hx j + ky j + lz j ) (hkl )]


j =1

The equation cannot be solved for the correct parameters in one go

Use an iterative process instead

Refinement iterations

2
R
'
=
w
(
F

k
F
)
Our goal is to minimize
hkl o
c
hkl

We can use an iterative least squares approach to give parameter


shifts that will lead to an improved agreement between |Fo| and |Fc|

The process is repeated until the suggested shifts are insignificantly


small
- usually considered to be achieved when parameter shift << standard deviation
- at this minimum, the derivative of R with respect to each parameter (xj, yj, zj
Bj) should be zero

Convergence

A refinement process is usually considered as finished when


convergence is reached
- when all parameter shifts << standard deviation

However, the process only works well if the starting model is


sufficiently good
- many local minima in which the refinement could get stuck

Other methods offer better chances to find the absolute minimum


from a bad starting model
- simulated annealing, random walk

False minima

Errors

The errors of all observations are included in the refinement process


via the weight factors
- weak or uncertain reflections will have less weight than strong reflections

The least squares output will proved esds (estimated standard


deviations) for all refined parameters

Watch out for high correlation coefficients


- correlation coefficients tell you whether two model parameters really are
independent

Judging the refinement

Statistical values are used to judge the goodness of a refinement

The level of agreement between observed and calculated structure


factors is often indicated by R factors and Goodness of Fit (GooF)
values
RF = ( Fo (hkl ) k Fc (hkl ) ) / | Fo (hkl ) |
hkl

hkl
2 2

wRF 2 = { [ w( Fo (hkl ) Fc (hkl ) ) ] / [ w | Fo (hkl ) |2 ]}1/ 2


2

hkl

hkl

GooF = S = { [ w( Fo (hkl ) Fc (hkl ) ) 2 ] /( n p )}1/ 2


2

hkl

- for n observations and p parameters

R factors

For a good small molecule refinement, the final RF values


are expected to be ~0.02-0.08

Placing random atoms in a unit cell is expected to give R


factors of 0.83 and 0.59 for centric and acentric space
groups, respectively

Obtaining RF < 0.20 usually means that the structural model


has no major errors in it

Refinement strategy

Unit cell constants need to be refined


- original indexing just gives approximate values

Atomic positions obtained by Patterson searches, direct methods or


other approaches should be refined
- look at interatomic distances to judge whether refined positions make sense
- atoms in special positions cannot move in all directions

Atomic displacement parameters should be varied


- can indicate wrong atomic weight: Zmodel > (<) Zreal leads to large (small) ADPs
- isotropic overall temperature factors can be obtained from Wilson plots as a
first approximation

Estimating the overall temperature factor

We know that observed structure factor magnitudes are smaller than


real values because of thermal motion and scaling issues
K Fo (hkl ) F (hkl ) = f e
2

2 2 B sin 2 / 2

ln[ Fo (hkl ) / f 2 ] = ln K 2 B sin 2 / 2


2

- for random atom placement in the unit cell

Both K and B can be obtained from a Wilson plot

Wilson plots

Restraints and constraints

It is possible to impose certain restrictions on the refinement due to


some knowledge that is not inherent in the diffraction data
- restraints and constraints

Chemical knowledge, such as bond distances and angles, can be used


as a restraint in a minimization procedure
- a restraint will make certain moves unfavorable, but will not prohibit them

Knowledge about molecular connectivity can be used


- e.g., a rigid aromatic ring can be described by three positional and three
rotational parameters instead of 4n parameters (n = number of atoms)
- this would be a rigid body constraint

When to use restraints and constraints

Restraints and constraints can improve your data to parameter ratio


by reducing the number of parameters or adding observations
- very useful if your data is limited or of low quality

They improve the convergence properties of your refinement and


may allow a refinement to converge to the correct answer even if the
starting model is poor
- they make potentially disastrous parameter changes (e.g., one carbon atom
moving so far that the aromatic ring will no longer be connected) unfavorable
or prohibit them altogether

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