- PDB-3odg: crystal structure of xanthosine phosphorylase bound with xanthine... -
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Open data
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Basic information
Entry
Database: PDB / ID: 3odg
Title
crystal structure of xanthosine phosphorylase bound with xanthine from Yersinia pseudotuberculosis
Components
Xanthosine phosphorylase
Keywords
TRANSFERASE / Structural Genomics / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC / Purine Nucleoside Phosphorylase / purine nucleoside binding
Function / homology
Function and homology information
nucleoside metabolic process / purine-nucleoside phosphorylase / purine-nucleoside phosphorylase activity / cytoplasm Similarity search - Function
Resolution: 1.64→48.24 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.964 / SU B: 4.259 / SU ML: 0.065 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.18727
1560
5 %
RANDOM
Rwork
0.15518
-
-
-
obs
0.15689
29504
97.02 %
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all
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30354
-
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parameters
Biso mean: 24.427 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.07 Å2
-0.03 Å2
0 Å2
2-
-
-0.07 Å2
0 Å2
3-
-
-
0.1 Å2
Refinement step
Cycle: LAST / Resolution: 1.64→48.24 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2059
0
12
252
2323
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.015
0.022
2125
X-RAY DIFFRACTION
r_angle_refined_deg
1.448
1.988
2881
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.613
5
274
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
37.551
24.684
79
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
13.534
15
358
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
14.618
15
7
X-RAY DIFFRACTION
r_chiral_restr
0.111
0.2
329
X-RAY DIFFRACTION
r_gen_planes_refined
0.01
0.021
1585
X-RAY DIFFRACTION
r_mcbond_it
0.991
1.5
1362
X-RAY DIFFRACTION
r_mcangle_it
1.703
2
2202
X-RAY DIFFRACTION
r_scbond_it
2.859
3
763
X-RAY DIFFRACTION
r_scangle_it
4.779
4.5
679
LS refinement shell
Resolution: 1.639→1.682 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.264
91
-
Rwork
0.235
1711
-
obs
-
-
76.98 %
Refinement TLS params.
Method: refined / Origin x: -28.102 Å / Origin y: -19.958 Å / Origin z: -0.107 Å
11
12
13
21
22
23
31
32
33
T
0.0046 Å2
0.0028 Å2
0.0009 Å2
-
0.0117 Å2
-0.0144 Å2
-
-
0.3068 Å2
L
0.8557 °2
-0.0526 °2
-0.0176 °2
-
0.8319 °2
0.1633 °2
-
-
0.3095 °2
S
-0.0122 Å °
-0.026 Å °
0.0671 Å °
0.033 Å °
0.0464 Å °
-0.1531 Å °
0.0044 Å °
0.0477 Å °
-0.0342 Å °
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