data_reporting_guidelines.md

Data reporting guidelines

After you have completed production, purification, kinetic assay, and thermal denaturation assay on your batch of mutants, you have a lot of data for each mutant.

Here's how to interpret the data and write a short scientific report describing your findings. An example report can be found in example_report.md.

For each mutant, the following things should be included. Each item has a one-word name, a brief description including a unit of measurement (if necessary), and an example of use. Sometimes there is more than one example.

mutant_name

The mutant name

E164A

researcher

Name of the undergraduate student researcher who did the work.

One or more names

Alex

Amy, Ryan A., Ryan B.

box

The physical location of the plasmid encoding this mutant, box number.

Numerical index

2

row

The physical location of the plasmid encoding this mutant, row letter.

Alphanumerical index

B

column

The physical location of the plasmid encoding this mutant, column number. (A lot of the boxes only have columns up to 9.)

Numerical index

8

expression

Does the mutant appear on a gel after 2 independent attempts to produce and purify?

Note: if the mutant does not express, only the next section (gel image) is relevant. For all other sections, the entry is "NaN".

1 for yes, 0 for no

0

gel_number

The index of the gel that this mutant appears on. Gels for a given data set are labeled in order from 1. Gel images should be saved on the gel imaging computer completely labeled. Ladder should be labeled with its name, e.g. "Thermo PAGE-Rule". Mutants should be labeled with their names. Wild type proteins should be labeled as "WT". It's not necessary to further distinguish wild type proteins.

Numerical index

4

protein_yield

Protein yield as assessed by A280. If the protein does not express, do not report A280 (or any of the following functional parameters).

mg/mL

1.28

kcat

The measured k_cat for this mutant, as determined by kinetic assay and fit using bagel.genomecenter.ucdavis.edu. The published limit of detection for our system is 1 min⁻¹. The maximum value for k_cat we have observed so far is 1.1 × 10⁴ min⁻¹ (R240A), and the wild type BglB protein has a k_cat of 8.8 × 10³ min⁻¹ to an error of about 5%.

min⁻¹

1.44e3

834.23

3.4

kcat_err

The measured standard error (one standard deviation error) of the fit to the Michaelis-Menten equation as determined by kinetic assay for the kcat parameter.

1.3e2

6.22

0.13

km

The measured K_M for this mutant as determined by kinetic assay (see "kcat" for more).

mM

5.52

0.21

15.50

km_err

The measured standard error (one standard deviation error) of the fit to the Michaelis-Menten equation as determined by kinetic assay for the KM parameter.

0.43

kcatkm

Measured kcat/km. ("<10" for mutants with activity below LOD, linear fit, or kcat/(1e-3*KM)

M⁻¹min⁻¹

1.74e5

918.3

<10

kcatkm_err

Standard error (1 std. dev.) for the quotient kcat/KM. The standard error for ranges such as <10 should be reported as "NaN". You may recall that for a quotient Q=a/x, the uncertainty sigma(Q) can be calculated as abs(Q)*sqrt((sigma(a)/a)^2+(sigma(x)/x)^2)) when the standard errors sigma(a) and sigma(x) are known.

M⁻¹min⁻¹

1.2e2

5591.2

tm

Measured functional protein melting temperature T_m as determined by thermal stability assay.

˚C

39.2

tm_err

Standard error (1 std. dev.), Tm

C

3.1

data_complete

Data for this mutant is complete. Is the data for this mutant 100% correct and complete?

1 for yes and 0 for no (default: 0)

1

FAQ

Why are all the names lowercased single words with underscores instead of spaces?

The names are formatted this way to make nicely-named header columns in a pandas DataFrame.