BIOMOLECULE: 1 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION ... BIOMOLECULE: 1 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. CRYSTAL PACKING ANALYSIS SUGGESTS A MONOMER IN THE SOLUTION. SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUGGESTS THAT A HEXAMER MAY BE THE SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION BUT IT MAY BE UNSTABLE.
Remark 999
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.
CRYSTAL PACKING ANALYSIS SUGGESTS A MONOMER IN THE SOLUTION STATE. SIZE EXCLUSION CHROMATOGRAPHY SUGGESTS THAT A HEXAMER MAY BE THE SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION BUT IT MAY BE UNSTABLE.
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
0.91837
1
2
0.97929
1
3
0.97905
1
反射
解像度: 2→29.013 Å / Num. obs: 28915 / % possible obs: 99.3 % / 冗長度: 7.35 % / Biso Wilson estimate: 34.26 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 13.75
反射 シェル
解像度 (Å)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Diffraction-ID
% possible all
2-2.07
0.519
2.57
19575
1
95.4
2.07-2.15
0.38
3.5
20943
1
100
2.15-2.25
0.266
5
22033
1
99.9
2.25-2.37
0.198
6.5
21868
1
100
2.37-2.52
0.15
8.5
21915
1
100
2.52-2.71
0.104
11.8
21176
1
100
2.71-2.99
0.074
15.8
22151
1
100
2.99-3.42
0.049
22.1
21246
1
99.9
3.42-4.3
0.034
29.1
21149
1
100
4.3-29.013
0.027
32.4
20538
1
98.2
-
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
REFMAC
5.2.0019
精密化
PHENIX
精密化
SHELX
位相決定
MolProbity
3beta29
モデル構築
XSCALE
データスケーリング
PDB_EXTRACT
2
データ抽出
MAR345
CCD
データ収集
XDS
データ削減
SHELXD
位相決定
autoSHARP
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→29.013 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.945 / SU B: 7.78 / SU ML: 0.105 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.16 / ESU R Free: 0.145 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 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 4. PG4 MOLECULES FROM THE CRYSTALLIZATION CONDITION HAVE BEEN MODELED IN THE SOLVENT STRUCTURE.
Rfactor
反射数
%反射
Selection details
Rfree
0.218
1470
5.1 %
RANDOM
Rwork
0.184
-
-
-
all
0.185
-
-
-
obs
0.185
28893
99.88 %
-
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: 35.333 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.65 Å2
-0.33 Å2
0 Å2
2-
-
-0.65 Å2
0 Å2
3-
-
-
0.98 Å2
精密化ステップ
サイクル: LAST / 解像度: 2→29.013 Å
タンパク質
核酸
リガンド
溶媒
全体
原子数
2585
0
99
111
2795
拘束条件
Refine-ID
タイプ
Dev ideal
Dev ideal target
数
X-RAY DIFFRACTION
r_bond_refined_d
0.016
0.022
2820
X-RAY DIFFRACTION
r_bond_other_d
0.004
0.02
1960
X-RAY DIFFRACTION
r_angle_refined_deg
1.702
1.993
3802
X-RAY DIFFRACTION
r_angle_other_deg
1.304
3
4812
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
3.856
5
358
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
36.077
24.56
125
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
12.096
15
506
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
15.395
15
17
X-RAY DIFFRACTION
r_chiral_restr
0.101
0.2
433
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.02
3056
X-RAY DIFFRACTION
r_gen_planes_other
0.003
0.02
537
X-RAY DIFFRACTION
r_nbd_refined
0.184
0.3
552
X-RAY DIFFRACTION
r_nbd_other
0.14
0.3
1979
X-RAY DIFFRACTION
r_nbtor_refined
0.169
0.5
1329
X-RAY DIFFRACTION
r_nbtor_other
0.083
0.5
1405
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.176
0.5
166
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.093
0.3
17
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.169
0.3
72
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.157
0.5
19
X-RAY DIFFRACTION
r_mcbond_it
1.993
3
1757
X-RAY DIFFRACTION
r_mcbond_other
0.491
3
679
X-RAY DIFFRACTION
r_mcangle_it
3.133
5
2760
X-RAY DIFFRACTION
r_scbond_it
5.442
8
1198
X-RAY DIFFRACTION
r_scangle_it
7.653
11
1028
LS精密化 シェル
解像度: 2→2.054 Å / Total num. of bins used: 20
Rfactor
反射数
%反射
Rfree
0.298
120
-
Rwork
0.222
2006
-
obs
-
2126
99.44 %
精密化 TLS
手法: refined / Refine-ID: X-RAY DIFFRACTION
ID
L11 (°2)
L12 (°2)
L13 (°2)
L22 (°2)
L23 (°2)
L33 (°2)
S11 (Å °)
S12 (Å °)
S13 (Å °)
S21 (Å °)
S22 (Å °)
S23 (Å °)
S31 (Å °)
S32 (Å °)
S33 (Å °)
T11 (Å2)
T12 (Å2)
T13 (Å2)
T22 (Å2)
T23 (Å2)
T33 (Å2)
Origin x (Å)
Origin y (Å)
Origin z (Å)
1
3.3437
-2.3968
-1.6321
3.4478
1.8819
2.739
0.1382
-0.0279
0.658
-0.1541
0.2339
-0.3783
-0.2626
0.1986
-0.3721
-0.126
-0.0134
0.0078
-0.0311
0.0035
0.0522
44.892
16.3107
-7.3264
2
2.9629
0.6426
-0.3735
1.7014
0.0877
0.0653
-0.0757
0.2913
0.0995
-0.1826
0.0546
0.4432
-0.0943
0.0099
0.0211
-0.0626
0
-0.0878
0.0047
0.1317
0.0584
21.5941
7.6485
-4.5163
3
1.5212
-1.9669
-0.7496
3.1545
0.4839
0.7547
0.1104
0.0693
0.1884
-0.2276
-0.0952
-0.2161
-0.0177
-0.0354
-0.0152
-0.0634
-0.0459
-0.03
-0.0216
0.0134
-0.0792
34.3618
23.289
-6.2604
4
1.3811
0.8132
-0.9941
2.6883
-0.6201
3.196
0.1408
-0.1648
0.14
0.4378
-0.056
-0.0281
-0.2621
0.1621
-0.0848
-0.0352
-0.0136
-0.0249
-0.0105
0.0172
-0.0956
41.5408
5.669
15.0568
精密化 TLSグループ
Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A