AUTHORS STATE THAT CRYSTAL PACKING ANALYSIS SUPPORTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE. SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A MONOMER AS A SIGNIFICANT OLIGOMERIZATION STATE.
モノクロメーター: Single crystal Si(111) bent monochromator (horizontal focusing) 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
相対比: 1
反射
解像度: 2.25→29.037 Å / Num. obs: 22597 / % possible obs: 100 % / 冗長度: 7.2 % / Biso Wilson estimate: 38.144 Å2 / Rmerge(I) obs: 0.129 / Rsym value: 0.129 / Net I/σ(I): 4.9
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
2.25-2.31
7.3
0.815
0.9
12110
1648
0.815
100
2.31-2.37
7.4
0.735
1
11717
1593
0.735
100
2.37-2.44
7.3
0.609
1.3
11464
1561
0.609
100
2.44-2.52
7.4
0.528
1.4
11056
1499
0.528
100
2.52-2.6
7.3
0.473
1.6
10694
1460
0.473
100
2.6-2.69
7.3
0.408
1.9
10403
1417
0.408
100
2.69-2.79
7.3
0.326
2.3
10162
1384
0.326
100
2.79-2.9
7.3
0.254
3
9756
1329
0.254
100
2.9-3.03
7.3
0.195
3.8
9261
1270
0.195
100
3.03-3.18
7.3
0.149
4.9
8940
1227
0.149
100
3.18-3.35
7.3
0.119
6.1
8482
1168
0.119
100
3.35-3.56
7.2
0.106
6.4
8013
1108
0.106
100
3.56-3.8
7.2
0.094
7.1
7434
1035
0.094
100
3.8-4.11
7.1
0.082
7.8
6981
978
0.082
100
4.11-4.5
7.1
0.068
9
6388
903
0.068
100
4.5-5.03
7.1
0.066
9.4
5853
830
0.066
100
5.03-5.81
7
0.071
9.3
5169
743
0.071
100
5.81-7.12
6.8
0.076
8.4
4322
638
0.076
100
7.12-10.06
6.5
0.058
9.9
3296
507
0.058
100
10.06-29.04
5.8
0.06
10.1
1725
299
0.06
96
-
位相決定
位相決定
手法: 単波長異常分散
-
解析
ソフトウェア
名称
バージョン
分類
NB
REFMAC
5.2.0019
精密化
PHENIX
精密化
SHELX
位相決定
MolProbity
3beta29
モデル構築
SCALA
データスケーリング
PDB_EXTRACT
3.004
データ抽出
MOSFLM
データ削減
autoSHARP
位相決定
SHELXD
位相決定
精密化
構造決定の手法: 単波長異常分散 / 解像度: 2.25→29.037 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.942 / SU B: 9.298 / SU ML: 0.125 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.185 / ESU R Free: 0.176 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 RECORDS CONTAIN RESIDUAL B FACTORS ONLY. (3). A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING ...詳細: (1). HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. (2). ATOM RECORDS CONTAIN 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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. (4). ONE COENZYME A (COA) MONOMER WAS MODELED BASED ON THE PRESENCE OF CLEAR AND CONCLUSIVE ELECTRON DENSITY. (5). ETHYLENE GLYCOL (EDO) MOLECULES FROM CRYO SOLUTION WERE MODELED. (6). RESIDUES -5 THROUGH -11 OF THE N-TERMINAL PURIFICATION TAG ARE LOCATED IN POOR DENSITY.
Rfactor
反射数
%反射
Selection details
Rfree
0.221
1154
5.1 %
RANDOM
Rwork
0.168
-
-
-
obs
0.171
22552
99.92 %
-
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: 31.366 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-1.8 Å2
0 Å2
0 Å2
2-
-
-1.8 Å2
0 Å2
3-
-
-
3.6 Å2
精密化ステップ
サイクル: LAST / 解像度: 2.25→29.037 Å
タンパク質
核酸
リガンド
溶媒
全体
原子数
2253
0
68
175
2496
拘束条件
Refine-ID
タイプ
Dev ideal
Dev ideal target
数
X-RAY DIFFRACTION
r_bond_refined_d
0.015
0.022
2446
X-RAY DIFFRACTION
r_bond_other_d
0.002
0.02
1756
X-RAY DIFFRACTION
r_angle_refined_deg
1.635
2.001
3301
X-RAY DIFFRACTION
r_angle_other_deg
0.957
3
4236
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.586
5
296
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
28.615
22.566
113
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
15.522
15
438
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
19.683
15
25
X-RAY DIFFRACTION
r_chiral_restr
0.088
0.2
345
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.02
2700
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
528
X-RAY DIFFRACTION
r_nbd_refined
0.199
0.2
436
X-RAY DIFFRACTION
r_nbd_other
0.203
0.2
1862
X-RAY DIFFRACTION
r_nbtor_refined
0.182
0.2
1163
X-RAY DIFFRACTION
r_nbtor_other
0.089
0.2
1342
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.147
0.2
148
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.16
0.2
8
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.317
0.2
39
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.139
0.2
18
X-RAY DIFFRACTION
r_mcbond_it
2.035
3
1585
X-RAY DIFFRACTION
r_mcbond_other
0.473
3
589
X-RAY DIFFRACTION
r_mcangle_it
2.894
5
2330
X-RAY DIFFRACTION
r_scbond_it
5.384
8
1104
X-RAY DIFFRACTION
r_scangle_it
6.637
11
971
LS精密化 シェル
解像度: 2.25→2.308 Å / Total num. of bins used: 20
Rfactor
反射数
%反射
Rfree
0.28
86
-
Rwork
0.232
1561
-
all
-
1647
-
obs
-
-
100 %
精密化 TLS
手法: refined / Origin x: 29.3437 Å / Origin y: 4.7224 Å / Origin z: -0.1209 Å