Journal: To be Published Title: Structural insight into nucleotide rhamnose synthase/epimerase-reductase from Arabidopsis thaliana Authors: Han, X. / Liu, X.
Method to determine structure: SAD / Resolution: 2.7→41.779 Å / SU ML: 0.38 / σ(F): 1.34 / Phase error: 27.68 / Stereochemistry target values: ML Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2652
3485
10.03 %
RANDOM
Rwork
0.1985
-
-
-
all
0.247
-
-
-
obs
0.2051
34735
94.42 %
-
Solvent computation
Shrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.022 Å2 / ksol: 0.352 e/Å3
Displacement parameters
Baniso -1
Baniso -2
Baniso -3
1-
1.3851 Å2
0 Å2
-0 Å2
2-
-
6.5156 Å2
-0 Å2
3-
-
-
-7.9008 Å2
Refinement step
Cycle: LAST / Resolution: 2.7→41.779 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
4270
0
14
68
4352
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.009
4358
X-RAY DIFFRACTION
f_angle_d
1.179
5899
X-RAY DIFFRACTION
f_dihedral_angle_d
15.96
1599
X-RAY DIFFRACTION
f_chiral_restr
0.078
668
X-RAY DIFFRACTION
f_plane_restr
0.007
748
LS refinement shell
Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 25
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
% reflection obs (%)
2.603-2.6386
0.4012
131
0.2668
1168
89
2.6386-2.6763
0.3653
137
0.2711
1220
92
2.6763-2.7163
0.3427
147
0.2531
1283
95
2.7163-2.7587
0.351
147
0.2645
1259
98
2.7587-2.8039
0.3531
154
0.2597
1347
100
2.8039-2.8523
0.3041
142
0.2545
1309
100
2.8523-2.9041
0.3567
150
0.2416
1316
100
2.9041-2.96
0.3404
151
0.2475
1340
100
2.96-3.0204
0.3333
143
0.2396
1308
100
3.0204-3.086
0.3319
154
0.2468
1360
100
3.086-3.1578
0.3262
142
0.2154
1294
100
3.1578-3.2367
0.3201
147
0.2309
1336
100
3.2367-3.3242
0.2495
150
0.1945
1332
100
3.3242-3.422
0.3167
147
0.2063
1308
100
3.422-3.5324
0.3103
147
0.2048
1329
100
3.5324-3.6586
0.3955
95
0.2002
863
95
3.6586-3.8049
0.2298
77
0.231
729
94
3.8049-3.978
0.2514
144
0.206
1241
95
3.978-4.1875
0.2588
140
0.1681
1292
98
4.1875-4.4496
0.1928
142
0.1489
1309
97
4.4496-4.7927
0.1698
144
0.1351
1270
97
4.7927-5.2742
0.2009
143
0.1569
1305
99
5.2742-6.0354
0.2406
142
0.176
1318
99
6.0354-7.5965
0.2393
144
0.1903
1301
98
7.5965-41.7847
0.2151
125
0.2068
1115
84
+
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