- PDB-2oe5: 1.5 A X-ray crystal structure of Apramycin complex with RNA fragm... -
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基本情報
登録情報
データベース: PDB / ID: 2oe5
タイトル
1.5 A X-ray crystal structure of Apramycin complex with RNA fragment GGCGUCGCUAGUACCG/GGUACUAAAAGUCGCCC containing the human ribosomal decoding A site: RNA construct with 3'-overhang
SEQUENCE THE RESIDUES THAT ARE NATURALLY OCCURING IN THE HUMAN RIBOSOMAL DECODING A SITE ARE ...SEQUENCE THE RESIDUES THAT ARE NATURALLY OCCURING IN THE HUMAN RIBOSOMAL DECODING A SITE ARE NUMBERED 1404-1413 (CHAIN A) AND 1487-1497 (CHAIN B). THIS NUMBERING IS ADAPTED FROM THE BACTERIAL ESCHERICHIA COLI SEQUENCE. IN BOTH STRANDS TERMINAL RESIDUES ARE DISTINCT FROM HUMAN AND WERE INCORPORATED FOR CRYSTALLIZATION PURPOSES. THE INCORPORATED RESIDUES ARE NUMBERED 2-3, 14-17 (CHAIN A) AND 84-86,98-100 (CHAIN B).
構造決定の手法: 分子置換 開始モデル: STANDARD RNA-MODEL BUILT IN TURBO-FRODO 解像度: 1.51→19.92 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.029 / SU ML: 0.072 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.097 / ESU R Free: 0.094 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD 詳細: THE SO4 ION IS PARTIALLY DISORDERED AND IT WAS REFINED WITH OCCUPANCY 0.5
Rfactor
反射数
%反射
Selection details
Rfree
0.2268
692
5 %
RANDOM
Rwork
0.19876
-
-
-
obs
0.20006
13173
92.73 %
-
all
-
13173
-
-
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: 1.4 Å / 溶媒モデル: BABINET MODEL WITH MASK
原子変位パラメータ
Biso mean: 20.524 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.02 Å2
0 Å2
0 Å2
2-
-
-0.06 Å2
0 Å2
3-
-
-
0.04 Å2
精密化ステップ
サイクル: LAST / 解像度: 1.51→19.92 Å
タンパク質
核酸
リガンド
溶媒
全体
原子数
0
698
44
164
906
拘束条件
Refine-ID
タイプ
Dev ideal
Dev ideal target
数
X-RAY DIFFRACTION
r_bond_refined_d
0.014
0.021
827
X-RAY DIFFRACTION
r_bond_other_d
0
0.02
297
X-RAY DIFFRACTION
r_angle_refined_deg
1.793
3
1283
X-RAY DIFFRACTION
r_angle_other_deg
1.746
3
779
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
X-RAY DIFFRACTION
r_chiral_restr
0.871
0.2
149
X-RAY DIFFRACTION
r_gen_planes_refined
0.011
0.02
344
X-RAY DIFFRACTION
r_gen_planes_other
0
0.02
1
X-RAY DIFFRACTION
r_nbd_refined
0.124
0.3
80
X-RAY DIFFRACTION
r_nbd_other
0.206
0.3
391
X-RAY DIFFRACTION
r_nbtor_refined
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.216
0.5
110
X-RAY DIFFRACTION
r_xyhbond_nbd_other
0.05
0.5
3
X-RAY DIFFRACTION
r_metal_ion_refined
0.065
0.5
2
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.112
0.3
8
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.203
0.3
15
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.247
0.5
16
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
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
X-RAY DIFFRACTION
r_scbond_it
1.873
3
827
X-RAY DIFFRACTION
r_scangle_it
2.535
4.5
1283
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS精密化 シェル
解像度: 1.51→1.544 Å / Total num. of bins used: 20 /
Rfactor
反射数
Rfree
0.35
59
Rwork
0.354
888
精密化 TLS
手法: refined / Origin x: 18.6988 Å / Origin y: -2.0052 Å / Origin z: 43.4683 Å