Table 2

Quality of the model. A: Parameters reflecting the quality of the model checked by «WHAT IF» [29]. B: Quality of chain of the model. The model is verified at 2Å resolution. Parameter values in the table represent observed values for the GBV-C polymerase model compared with typical values obtained for well refined structures at the same resolution [28].

A

Structure Z-scores:

1st generation packing quality

-1.577

2nd generation packing quality

-2.94

Ramachandran plot appearance

-0.74

chi-1/chi-2 rotamer normality

-0.224

Backbone conformation

-0.904

RMS Z-scores, should be close to 1.0:

Bond lengths

0.950

Bond angles

1.426

Omega angle restraints

-0.923

Inside/Outside distribution

1.096

B

Stereochemical parameter

N° of data

points Parameter

valueTypical

valueBand width

N° of bandwidth

Stereochemistry of main-chain

Percentage residues in A, B, L

438

89

83.8

10

0.5

Omega angle S.D

507

6.8

6

3

0.3

Bad contacts 100 residues

3

0.6

4.2

10

-0.4

Zeta angle S.D.

476

2.8

3.1

1.6

-0.2

Hydrogen bond energy S.D.

305

0.7

0.8

0.2

-0.4

Stereochemistry of side-chain

Chi-1 gauche minus S.D.

79

15.7

18.1

6.5

-0.4

Chi-1 trans S.D.

103

13.2

19

5.3

-1.1

Chi-1 gauche plus S.D.

205

11.4

17.5

4.9

-1.2

Chi-1 pooled S.D.

387

13

18.2

4.8

-1.1

Chi-2 trans S.D.

114

15.7

20.4

5

-0.9

Ferron et al. BMC Bioinformatics 2005 6:255   doi:10.1186/1471-2105-6-255