Crystal structure of pleckstrin homology domain (YP_926556.1) from SHEWANELLA AMAZONENSIS SB2B at 1.99 A resolution
要素
pleckstrin homology domain
キーワード
structural genomics / unknown function / YP_926556.1 / pleckstrin homology domain / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / Protein of unknown function (DUF1696)
1. THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED ...1. 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. 2. THE PROTEIN WAS REDUCTIVELY METHYLATED PRIOR TO CRYSTALLIZATION.
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実験情報
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実験
実験
手法: X線回折 / 使用した結晶の数: 2
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試料調製
結晶
マシュー密度: 2.07 Å3/Da / 溶媒含有率: 40.61 % 解説: THE STRUCTURE WAS SOLVED BY MAD METHOD USING FOUR DATASETS COLLECTED FROM TWO CRYSTALS. THE SHARP OUTPUT PHASES WERE USED AS RESTRAINTS DURING REFINEMENT.
解像度: 1.99→47.351 Å / Num. obs: 41702 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / 冗長度: 3.61 % / Biso Wilson estimate: 22.653 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 10.18
反射 シェル
解像度 (Å)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Num. unique obs
Diffraction-ID
% possible all
1.99-2.06
0.531
2.3
14883
4075
1,2
99.1
2.06-2.14
0.408
3
14594
3949
1,2
98.4
2.14-2.24
0.314
3.8
15552
4233
1,2
98.1
2.24-2.36
0.248
4.8
15401
4209
1,2
99.5
2.36-2.51
0.204
5.8
15358
4180
1,2
99
2.51-2.7
0.155
7.6
14852
4067
1,2
98.9
2.7-2.97
0.109
10.3
15139
4180
1,2
99
2.97-3.4
0.071
15
15083
4194
1,2
98.5
3.4-4.27
0.043
22.2
14856
4184
1,2
97.9
4.27-47.351
0.04
25.6
15011
4423
1,2
96
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位相決定
位相決定
手法: 多波長異常分散
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解析
ソフトウェア
名称
バージョン
分類
NB
REFMAC
5.5.0092
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
3.006
データ抽出
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: 1.99→47.351 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.92 / Occupancy max: 1 / Occupancy min: 0.23 / SU B: 8.591 / SU ML: 0.11 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.193 / ESU R Free: 0.168 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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 4. GLYCEROL (GOL) AND POLY ETHYLENE GLYCOL FRAGMENTS (PEG,PGE) MODELED ARE PRESENT IN CRYSTALLIZATION/CRYO CONDITIONS.
Rfactor
反射数
%反射
Selection details
Rfree
0.233
2115
5.1 %
RANDOM
Rwork
0.189
-
-
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obs
0.191
41641
98.47 %
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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