High-resolution crystal structure Streptococcus pyogenes beta-NAD+ glycohydrolase in complex with its endogenous inhibitor IFS reveals a water-rich interface
Method to determine structure: SAD / Resolution: 1.71→20 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.594 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.23519
4140
5 %
RANDOM
Rwork
0.19722
-
-
-
obs
0.19913
78603
93.52 %
-
all
-
82755
-
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Biso mean: 29.032 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.1 Å2
0.01 Å2
0.09 Å2
2-
-
0.01 Å2
0.05 Å2
3-
-
-
-0.14 Å2
Refinement step
Cycle: LAST / Resolution: 1.71→20 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
6708
0
0
596
7304
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.01
0.02
6832
X-RAY DIFFRACTION
r_angle_refined_deg
1.333
1.963
9174
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.478
5
826
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
33.851
24.97
330
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
13.682
15
1312
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
18.365
15
30
X-RAY DIFFRACTION
r_chiral_restr
0.094
0.2
982
X-RAY DIFFRACTION
r_gen_planes_refined
0.007
0.02
5094
LS refinement shell
Resolution: 1.705→1.749 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.317
278
-
Rwork
0.261
5114
-
obs
-
-
82.8 %
+
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