温度: 291 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 5.5 詳細: Final droplet composition: 0.5 mM oligonucleotide, 5% MPD, 20 mM sodium cacodylate, pH 5.5, 10 mM cobalt hexamine, 20 mM LiCl and 10 mM MgCl2., VAPOR DIFFUSION, HANGING DROP, temperature 291K
解像度: 1.61→1.66 Å / Rmerge(I) obs: 0.53 / % possible all: 0.969
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解析
ソフトウェア
名称
バージョン
分類
REFMAC
5.2.0003
精密化
X-GEN
データ削減
X-GEN
データスケーリング
EPMR
位相決定
精密化
構造決定の手法: 分子置換 開始モデル: Model of native A-RNA 解像度: 1.61→24.78 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.959 / SU B: 5.698 / SU ML: 0.088 / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.206 / ESU R Free: 0.113 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD / 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
反射数
%反射
Selection details
Rfree
0.231
558
7.5 %
RANDOM
Rwork
0.196
-
-
-
all
0.199
7538
-
-
obs
0.199
7425
98.55 %
-
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: BABINET MODEL WITH MASK
原子変位パラメータ
Biso mean: 27.11 Å2
Baniso -1
Baniso -2
Baniso -3
1-
1.03 Å2
0.52 Å2
0 Å2
2-
-
1.03 Å2
0 Å2
3-
-
-
-1.55 Å2
精密化ステップ
サイクル: LAST / 解像度: 1.61→24.78 Å
タンパク質
核酸
リガンド
溶媒
全体
原子数
0
506
0
84
590
拘束条件
Refine-ID
タイプ
Dev ideal
Dev ideal target
数
X-RAY DIFFRACTION
r_bond_refined_d
0.012
0.021
564
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
200
X-RAY DIFFRACTION
r_angle_refined_deg
2.066
3.007
860
X-RAY DIFFRACTION
r_angle_other_deg
1.504
3
524
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
0.092
0.2
116
X-RAY DIFFRACTION
r_gen_planes_refined
0.019
0.02
246
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
0.182
0.2
89
X-RAY DIFFRACTION
r_nbd_other
0.281
0.2
279
X-RAY DIFFRACTION
r_nbtor_refined
0.251
0.2
224
X-RAY DIFFRACTION
r_nbtor_other
0.131
0.2
130
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.356
0.2
53
X-RAY DIFFRACTION
r_xyhbond_nbd_other
0.422
0.2
2
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.086
0.2
14
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.177
0.2
19
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.311
0.2
17
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
4.323
3
798
X-RAY DIFFRACTION
r_scangle_it
5.042
4.5
860
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: 1.61→1.648 Å / Total num. of bins used: 20
Rfactor
反射数
%反射
Rfree
0.265
42
-
Rwork
0.232
497
-
obs
-
539
97.12 %
精密化 TLS
手法: refined / Origin x: 4.4067 Å / Origin y: 12.3175 Å / Origin z: 14.3016 Å