タイプ: Cyclic peptide / クラス: 抗生剤 / 分子量: 1159.461 Da / 分子数: 1 / 由来タイプ: 天然 詳細: GRAMICIDIN S IS A DECAPEPTIDE, RESIDUES 1 AND 10 FORM A PEPTIDE BOND RESULTING IN CYCLIZATION. 由来: (天然) Brevibacillus brevis (バクテリア) / 参照: GRAMICIDIN S
GRAMICIDIN S IS A CYCLODECAPEPTIDE, CONSTRUCTED AS TWO IDENTICAL PENTAPEPTIDES JOINED HEAD TO TAIL, ...GRAMICIDIN S IS A CYCLODECAPEPTIDE, CONSTRUCTED AS TWO IDENTICAL PENTAPEPTIDES JOINED HEAD TO TAIL, PRODUCED BY THE GRAM POSITIVE BACTERIUM BACILLUS BREVIS HERE, GRAMICIDIN S IS REPRESENTED BY THE SEQUENCE (SEQRES)
プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長
波長: 1.5406 Å / 相対比: 1
反射
解像度: 0.98→22.34 Å / Num. obs: 4028 / % possible obs: 81.1 % / Net I/σ(I): 210
-
解析
ソフトウェア
名称: REFMAC / バージョン: 5.8.0411 / 分類: 精密化
精密化
構造決定の手法: AB INITIO PHASING / 解像度: 0.98→22.34 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.988 / SU B: 0.276 / SU ML: 0.015 / 交差検証法: FREE R-VALUE / ESU R: 0.026 / ESU R Free: 0.023 詳細: Hydrogens have been added in their riding positions. At this resolution the FreeR is often equal to the overall R factor
Rfactor
反射数
%反射
Selection details
Rfree
0.1318
205
5.089 %
Random selection
Rwork
0.14
3823
-
-
all
0.14
-
-
-
obs
-
4028
80.738 %
-
溶媒の処理
イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.2 Å / 溶媒モデル: MASK BULK SOLVENT
原子変位パラメータ
Biso mean: 8.88 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.064 Å2
0.032 Å2
0 Å2
2-
-
0.064 Å2
-0 Å2
3-
-
-
-0.208 Å2
精密化ステップ
サイクル: LAST / 解像度: 0.98→22.34 Å
タンパク質
核酸
リガンド
溶媒
全体
原子数
82
0
4
9
95
拘束条件
Refine-ID
タイプ
Dev ideal
Dev ideal target
数
X-RAY DIFFRACTION
r_bond_refined_d
0.021
0.012
97
X-RAY DIFFRACTION
r_bond_other_d
0.004
0.015
103
X-RAY DIFFRACTION
r_angle_refined_deg
2.196
1.624
134
X-RAY DIFFRACTION
r_angle_other_deg
0.881
1.564
238
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
7.751
5
12
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
9.574
10
15
X-RAY DIFFRACTION
r_dihedral_angle_6_deg
23.292
10
2
X-RAY DIFFRACTION
r_chiral_restr
1.735
0.2
16
X-RAY DIFFRACTION
r_gen_planes_refined
0.013
0.02
104
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
20
X-RAY DIFFRACTION
r_nbd_refined
0.244
0.2
9
X-RAY DIFFRACTION
r_symmetry_nbd_other
0.204
0.2
73
X-RAY DIFFRACTION
r_nbtor_refined
0.221
0.2
42
X-RAY DIFFRACTION
r_symmetry_nbtor_other
0.168
0.2
60
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.119
0.2
3
X-RAY DIFFRACTION
r_nbd_other
0.114
0.2
12
X-RAY DIFFRACTION
r_symmetry_xyhbond_nbd_refined
0.118
0.2
3
X-RAY DIFFRACTION
r_mcbond_it
1.023
0.62
46
X-RAY DIFFRACTION
r_mcbond_other
1.02
0.62
45
X-RAY DIFFRACTION
r_mcangle_it
1.336
1.126
58
X-RAY DIFFRACTION
r_mcangle_other
1.332
1.122
59
X-RAY DIFFRACTION
r_scbond_it
2.916
0.965
51
X-RAY DIFFRACTION
r_scbond_other
2.927
0.98
50
X-RAY DIFFRACTION
r_scangle_it
4.176
1.583
76
X-RAY DIFFRACTION
r_scangle_other
4.228
1.597
74
X-RAY DIFFRACTION
r_lrange_it
4.488
8.265
87
X-RAY DIFFRACTION
r_lrange_other
4.54
8.032
87
LS精密化 シェル
Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20