Table 2 Statistics of X-ray diffraction data collection of AncLAAO-N5 for native and substrate binding forms (L-Gln, L-Trp, and L-Phe binding form).

From: Ancestral L-amino acid oxidases for deracemization and stereoinversion of amino acids

 

Native

Iodide-SAD

L-Gln binding

L-Trp binding

L-Phe binding

Space group

I422

I422

I422

I422

I422

Unit cell parameters

  a (Å)

131.9

132.6

132.6

132.5

132.0

  b (Å)

131.9

132.6

132.6

132.5

132.0

  c (Å)

191.2

191.9

191.8

191.7

191.4

  α (degree)

90.0

90.0

90.0

90.0

90.0

  β (degree)

90.0

90.0

90.0

90.0

90.0

  γ (degree)

90.0

90.0

90.0

90.0

90.0

  X-ray source

BL5A (PF)

BL5A (PF)

BL5A (PF)

BL5A (PF)

BL5A (PF)

  Wavelength (Å)

1.00

1.70

1.00

1.00

1.00

  Resolution (Å)

46.6-2.4 (2.49-2.40)

48.0-2.6 (2.74-2.60)

48.0-2.6 (2.74-2.60)

47.9-2.4 (2.53-2.4)

47.8-2.2 (2.32-2.20)

  No. of reflectionsa

877,891

2,780,097

704,737

899,166

1,156,916

  No. of unique   reflections

33,315

26,611

26,591

33,554

43,030

  Completeness (%)

100 (99.9)

100 (100)

100 (99.9)

100 (99.9)

100 (99.8)

  I/sig(I)

25.9 (5.5)

58.9 (16.0)

26.5 (6.2)

30.8 (6.6)

28.9 (7.0)

  CC1/2

0.999 (0.967)

1.00 (0.998)

1.00 (0.953)

1.00 (0.966)

1.00 (0.978)

  Rmergeb

0.125 (0.674)

0.085 (0.380)

0.119 (0.687)

0.107 (0.596)

0.107 (0.597)

  B of Wilson plot (Å)2

29.5

41.8

39.7

30.8

24.2

  Iodide sites

 

39

   

  FOM before DMc

 

0.38

   

  FOM after DMc

 

0.69

   

  Rd

0.171

 

0.207

0.208

0.173

  Rfreee

0.231

 

0.276

0.270

0.211

 RMSD of geometry

     

  Bond length (Å)

0.008

 

0.009

0.008

0.008

  Bond angle (degree)

0.92

 

1.04

0.92

0.88

 Geometry

     

  Ramachandran outlier (%)

0.5

 

0.7

0.3

0.3

  Ramachandran favored (%)

99.5

 

99.3

99.7

99.7

 Average B factor (Å)2

     

  Protein atoms

37.9

 

44.1

37.8

34.4

  Ligand atoms

30.8

 

41.3

33.3

29.5

  Solvent atoms

35.7

 

39.6

36.3

35.4

  PDB code

7C4K

 

7C4L

7C4M

7C4N

  1. a Sigma cutoff was set to none (F > 0σF).
  2. b Rmerge = ΣhΣi | Ii(h)−<I(h)> | / Σh I(h), where Ii(h) is the ith measurement of reflection h, and <I(h)> is the mean value of the symmetry-related reflection intensities. Values in brackets are for the shell of the highest resolution.
  3. c FOM before/after DM means that the figure of merit before/after density modification.
  4. d R = Σ | | Fo | −|Fc |  | / Σ | Fo | , where Fo and Fc are the observed and calculated structure factors used in the refinement, respectively.
  5. e Rfree is the R-factor calculated using 5% of the reflections chosen at random and omitted from the refinement.
  6. f n.d., not determined.