SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.
マシュー密度: 3.61 Å3/Da / 溶媒含有率: 65.66 % 解説: AFTER THE INITIAL TRACE, A MODEL OF A HOMOLOGOUS PROTEIN (PDB ENTRY 2GVK) WAS USED TO FACILITATE COMPLETION OF THE MODEL.
モノクロメーター: Single crystal Si(111) bent monochromator (horizontal focusing) プロトコル: MAD / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長
ID
波長 (Å)
相対比
1
0.979291
1
2
0.91837
1
3
0.97894
1
反射
解像度: 2.75→29.54 Å / Num. obs: 13932 / % possible obs: 95.4 % / Biso Wilson estimate: 58.902 Å2 / Rmerge(I) obs: 0.107 / Net I/σ(I): 10.85
反射 シェル
Diffraction-ID: 1
解像度 (Å)
最高解像度 (Å)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Num. unique all
% possible all
2.75-2.85
0.835
1.7
8805
2297
86.7
2.85-2.96
0.671
2.2
8529
2214
89.8
2.96-3.1
0.543
2.7
9500
2459
92.1
3.1-3.26
0.4
3.6
9309
2415
94.5
3.26-3.46
0.266
5.3
9345
2423
96.8
3.46-3.73
0.152
8.5
9908
2573
98.4
3.73-4.1
0.083
13.9
9809
2542
99.3
4.1-4.69
0.056
18.6
9839
2559
99.3
4.69
0.057
19.1
9792
2569
99.6
-
位相決定
位相決定
手法: 多波長異常分散
-
解析
ソフトウェア
名称
バージョン
分類
NB
MolProbity
3beta29
モデル構築
REFMAC
5.2.0005
精密化
XSCALE
データスケーリング
PDB_EXTRACT
2
データ抽出
XDS
データ削減
SOLVE
位相決定
RESOLVE
位相決定
精密化
構造決定の手法: 多波長異常分散 / 解像度: 2.75→29.54 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.932 / SU B: 22.648 / SU ML: 0.213 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.474 / ESU R Free: 0.279 立体化学のターゲット値: MAXIMUM LIKELIHOOD WITH PHASES 詳細: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...詳細: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.7 TO ACCOUNT FOR THE REDUCED SCATTERING DUE TO PARTIAL S-MET INCORPORATION. 3. ADDITIONAL ELECTRON DENSITY WAS NOTED ADJACENT TO RESIDUE A20 BUT NOT MODELLED. 4. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY.
Rfactor
反射数
%反射
Selection details
Rfree
0.229
691
5 %
RANDOM
Rwork
0.191
-
-
-
obs
0.193
13888
99.72 %
-
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
原子変位パラメータ
Biso mean: 58.485 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-2 Å2
0 Å2
0 Å2
2-
-
-2 Å2
0 Å2
3-
-
-
3.99 Å2
精密化ステップ
サイクル: LAST / 解像度: 2.75→29.54 Å
タンパク質
核酸
リガンド
溶媒
全体
原子数
2453
0
0
48
2501
拘束条件
Refine-ID
タイプ
Dev ideal
Dev ideal target
数
X-RAY DIFFRACTION
r_bond_refined_d
0.01
0.022
2513
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
2179
X-RAY DIFFRACTION
r_angle_refined_deg
1.134
1.947
3394
X-RAY DIFFRACTION
r_angle_other_deg
0.615
3
5081
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.927
5
306
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
35.04
24.361
133
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
15.824
15
424
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
12.404
15
15
X-RAY DIFFRACTION
r_chiral_restr
0.063
0.2
352
X-RAY DIFFRACTION
r_gen_planes_refined
0.003
0.02
2843
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
526
X-RAY DIFFRACTION
r_nbd_refined
0.228
0.3
600
X-RAY DIFFRACTION
r_nbd_other
0.212
0.3
2312
X-RAY DIFFRACTION
r_nbtor_refined
0.198
0.5
1241
X-RAY DIFFRACTION
r_nbtor_other
0.093
0.5
1414
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.146
0.5
130
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.146
0.3
9
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.215
0.3
32
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.203
0.5
8
X-RAY DIFFRACTION
r_mcbond_it
2.67
3
1578
X-RAY DIFFRACTION
r_mcbond_other
0.532
3
622
X-RAY DIFFRACTION
r_mcangle_it
3.803
5
2452
X-RAY DIFFRACTION
r_scbond_it
2.574
3
1064
X-RAY DIFFRACTION
r_scangle_it
3.761
5
942
LS精密化 シェル
解像度: 2.749→2.82 Å / Total num. of bins used: 20
Rfactor
反射数
%反射
Rfree
0.375
54
-
Rwork
0.34
953
-
obs
-
1007
99.11 %
精密化 TLS
手法: refined / Origin x: 27.641 Å / Origin y: 27.514 Å / Origin z: 38.523 Å