mature B cell apoptotic process / xanthine biosynthetic process / negative regulation of penile erection / Purine salvage / Ribavirin ADME / negative regulation of circadian sleep/wake cycle, non-REM sleep / negative regulation of mucus secretion / penile erection / purine nucleoside binding / positive regulation of germinal center formation ...mature B cell apoptotic process / xanthine biosynthetic process / negative regulation of penile erection / Purine salvage / Ribavirin ADME / negative regulation of circadian sleep/wake cycle, non-REM sleep / negative regulation of mucus secretion / penile erection / purine nucleoside binding / positive regulation of germinal center formation / negative regulation of adenosine receptor signaling pathway / inosine biosynthetic process / histamine secretion / cytoplasmic vesicle lumen / 2'-deoxyadenosine deaminase activity / amide catabolic process / adenosine deaminase / hypoxanthine biosynthetic process / germinal center B cell differentiation / adenosine catabolic process / adenosine deaminase activity / hypoxanthine salvage / inhibition of non-skeletal tissue mineralization / deoxyadenosine catabolic process / dAMP catabolic process / adenosine metabolic process / AMP catabolic process / positive regulation of T cell differentiation in thymus / dATP catabolic process / negative regulation of leukocyte migration / mucus secretion / regulation of cell-cell adhesion mediated by integrin / response to purine-containing compound / embryonic digestive tract development / allantoin metabolic process / trophectodermal cell differentiation / GMP salvage / IMP salvage / positive regulation of smooth muscle contraction / Peyer's patch development / germinal center formation / negative regulation of mature B cell apoptotic process / AMP salvage / regulation of T cell differentiation in thymus / negative regulation of thymocyte apoptotic process / anchoring junction / positive regulation of alpha-beta T cell differentiation / alpha-beta T cell differentiation / positive regulation of T cell differentiation / regulation of T cell differentiation / positive regulation of heart rate / leukocyte migration / lung alveolus development / positive regulation of T cell receptor signaling pathway / thymocyte apoptotic process / B cell proliferation / T cell differentiation / smooth muscle contraction / : / response to vitamin E / positive regulation of calcium-mediated signaling / positive regulation of B cell proliferation / T cell activation / dendrite cytoplasm / liver development / calcium-mediated signaling / placenta development / lung development / negative regulation of inflammatory response / positive regulation of T cell activation / T cell differentiation in thymus / T cell receptor signaling pathway / in utero embryonic development / lysosome / response to hypoxia / cell adhesion / external side of plasma membrane / neuronal cell body / apoptotic process / negative regulation of apoptotic process / extracellular space / zinc ion binding / cytosol / cytoplasm Similarity search - Function
Resolution: 2.35→42.4 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.91 / SU B: 16.989 / SU ML: 0.188 / Cross valid method: THROUGHOUT / ESU R: 0.508 / ESU R Free: 0.274 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.24993
755
5.1 %
RANDOM
Rwork
0.18949
-
-
-
obs
0.1925
14116
98 %
-
all
-
14404
-
-
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: 31.089 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.06 Å2
0 Å2
0 Å2
2-
-
-0.1 Å2
0 Å2
3-
-
-
0.16 Å2
Refinement step
Cycle: LAST / Resolution: 2.35→42.4 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2796
0
5
136
2937
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.009
0.022
2862
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.122
1.963
3875
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.736
5
348
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
38.139
24.519
135
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
16.137
15
508
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
14.436
15
15
X-RAY DIFFRACTION
r_chiral_restr
0.078
0.2
420
X-RAY DIFFRACTION
r_gen_planes_refined
0.004
0.021
2173
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
0.358
1.5
1741
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
0.703
2
2819
X-RAY DIFFRACTION
r_scbond_it
1.175
3
1121
X-RAY DIFFRACTION
r_scangle_it
1.978
4.5
1056
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 2.35→2.411 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.324
44
-
Rwork
0.219
946
-
obs
-
-
91.67 %
Refinement TLS params.
Method: refined / Origin x: 13.831 Å / Origin y: -11.12 Å / Origin z: -16.069 Å
11
12
13
21
22
23
31
32
33
T
0.037 Å2
-0.0195 Å2
0.012 Å2
-
0.0487 Å2
-0.0273 Å2
-
-
0.0173 Å2
L
1.4608 °2
-0.1356 °2
-0.5712 °2
-
1.6699 °2
0.2734 °2
-
-
1.9001 °2
S
-0.0617 Å °
0.0429 Å °
-0.036 Å °
-0.0436 Å °
-0.0014 Å °
0.0197 Å °
0.0213 Å °
-0.0057 Å °
0.0631 Å °
+
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