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 FOLLOWED BY THE TARGET SEQUENCE.
モノクロメーター: Single crystal Si(111) bent (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
0.97931
1
2
0.91837
1
反射
解像度: 2→29.185 Å / Num. obs: 35353 / % possible obs: 98.8 % / 冗長度: 4.1 % / Biso Wilson estimate: 27.46 Å2 / Rmerge(I) obs: 0.101 / Rsym value: 0.101 / Net I/σ(I): 6.2
反射 シェル
Diffraction-ID: 1
解像度 (Å)
冗長度 (%)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured all
Num. unique all
Rsym value
% possible all
2-2.05
4.1
0.87
0.8
10662
2601
0.87
99.7
2.05-2.11
4.1
0.664
1.1
10370
2541
0.664
99.6
2.11-2.17
4.1
0.528
1.4
10158
2479
0.528
99.6
2.17-2.24
4.1
0.423
1.8
9999
2431
0.423
99.6
2.24-2.31
4.1
0.358
1.9
9447
2299
0.358
99.6
2.31-2.39
4.1
0.291
2.6
9262
2247
0.291
99.4
2.39-2.48
4.1
0.256
2.9
9002
2173
0.256
99.2
2.48-2.58
4.1
0.193
3.9
8598
2083
0.193
99
2.58-2.7
4.1
0.154
4.8
8281
2000
0.154
99.1
2.7-2.83
4.1
0.129
5.8
7978
1923
0.129
98.9
2.83-2.98
4.1
0.11
6.7
7554
1825
0.11
98.6
2.98-3.16
4.1
0.094
7.4
7121
1723
0.094
98.5
3.16-3.38
4.1
0.08
8.5
6769
1642
0.08
98.4
3.38-3.65
4.1
0.066
9.5
6175
1489
0.066
98.2
3.65-4
4.1
0.056
10.9
5881
1424
0.056
97.8
4-4.47
4.1
0.046
13.5
5138
1249
0.046
97.6
4.47-5.16
4.1
0.046
13.1
4601
1119
0.046
97.2
5.16-6.32
4.1
0.05
12.2
3852
949
0.05
97.4
6.32-8.94
4
0.045
13.2
2979
749
0.045
96.5
8.94-29.18
3.6
0.04
16
1469
407
0.04
89.1
-
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
SOLVE
位相決定
REFMAC
5.2.0005
精密化
SCALA
データスケーリング
PDB_EXTRACT
2
データ抽出
MAR345
CCD
データ収集
MOSFLM
データ削減
CCP4
(SCALA)
データスケーリング
精密化
構造決定の手法: 多波長異常分散 / 解像度: 2→29.185 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.942 / SU B: 6.174 / SU ML: 0.089 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.123 / ESU R Free: 0.125 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. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...詳細: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. 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 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. RAMACHANDRAN OUTLIER A151 IS LOCATED IN POOR DENSITY. 5. UNMODELED DENSITY NEAR RESIDUES A13, A41, A126 AND A208 MAY BE PART OF THE ACTIVE SITE.
Rfactor
反射数
%反射
Selection details
Rfree
0.212
1774
5 %
RANDOM
Rwork
0.171
-
-
-
all
0.173
-
-
-
obs
0.173
35338
98.46 %
-
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: 29.661 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.03 Å2
0 Å2
0 Å2
2-
-
-0.16 Å2
0 Å2
3-
-
-
0.13 Å2
精密化ステップ
サイクル: LAST / 解像度: 2→29.185 Å
タンパク質
核酸
リガンド
溶媒
全体
原子数
2421
0
5
281
2707
拘束条件
Refine-ID
タイプ
Dev ideal
Dev ideal target
数
X-RAY DIFFRACTION
r_bond_refined_d
0.017
0.022
2537
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
2348
X-RAY DIFFRACTION
r_angle_refined_deg
1.48
1.971
3473
X-RAY DIFFRACTION
r_angle_other_deg
0.847
3
5461
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.817
5
348
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
35.713
25.472
106
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
14.138
15
428
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
23.605
15
12
X-RAY DIFFRACTION
r_chiral_restr
0.091
0.2
423
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.02
2873
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
459
X-RAY DIFFRACTION
r_nbd_refined
0.206
0.2
490
X-RAY DIFFRACTION
r_nbd_other
0.17
0.2
2358
X-RAY DIFFRACTION
r_nbtor_refined
0.171
0.2
1298
X-RAY DIFFRACTION
r_nbtor_other
0.085
0.2
1559
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.153
0.2
192
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.123
0.2
9
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.185
0.2
51
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.224
0.2
15
X-RAY DIFFRACTION
r_mcbond_it
2.37
3
1700
X-RAY DIFFRACTION
r_mcbond_other
0.597
3
674
X-RAY DIFFRACTION
r_mcangle_it
3.567
5
2685
X-RAY DIFFRACTION
r_scbond_it
6.042
8
927
X-RAY DIFFRACTION
r_scangle_it
8.808
11
776
LS精密化 シェル
解像度: 2→2.052 Å / Total num. of bins used: 20
Rfactor
反射数
%反射
Rfree
0.288
129
-
Rwork
0.238
2455
-
obs
-
2584
99.46 %
精密化 TLS
手法: refined / Origin x: 48.562 Å / Origin y: 25.58 Å / Origin z: 27.409 Å