- PDB-4r1k: Crystal structure of a NTF2-like protein (EUBSIR_01394) from Euba... -
+
データを開く
IDまたはキーワード:
読み込み中...
-
基本情報
登録情報
データベース: PDB / ID: 4r1k
タイトル
Crystal structure of a NTF2-like protein (EUBSIR_01394) from Eubacterium siraeum DSM 15702 at 2.56 A resolution
要素
Uncharacterized protein
キーワード
STRUCTURAL GENOMICS / UNKNOWN FUNCTION / NTF2-like fold / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
機能・相同性
Protein of unknown function DUF5104 / Domain of unknown function (DUF5104) / Nuclear Transport Factor 2; Chain: A, - #50 / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / Uncharacterized protein
THIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 30-166 OF THE TARGET SEQUENCE.
モノクロメーター: single crystal Si(111) bent / 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
0.97939
1
2
0.91837
1
3
0.97882
1
反射
解像度: 2.56→42.844 Å / Num. obs: 11309 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 53.294 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 10.16
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 obs
% possible all
2.56-2.65
0.652
2.1
4245
1109
97.5
2.65-2.76
0.544
2.5
4217
1153
97.8
2.76-2.88
0.352
3.6
3713
1047
95.7
2.88-3.03
0.24
5.4
4488
1128
99
3.03-3.22
0.158
7.6
4513
1142
99.3
3.22-3.47
0.115
10.2
4444
1142
98.3
3.47-3.82
0.09
12.6
4263
1145
98.7
3.82-4.37
0.06
16.8
3857
1087
94.4
4.37-5.48
0.053
19.8
4446
1143
98.6
5.48
0.051
20.4
4287
1172
96.1
-
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
PDB_EXTRACT
3.1
データ抽出
SHELX
位相決定
SHARP
位相決定
XSCALE
データスケーリング
REFMAC
5.7.0032
精密化
XDS
データ削減
SHELXD
位相決定
精密化
構造決定の手法: 多波長異常分散 / 解像度: 2.56→42.844 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.872 / Occupancy max: 1 / Occupancy min: 0.75 / SU B: 29.488 / SU ML: 0.288 / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.735 / ESU R Free: 0.357 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 SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE ...詳細: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. 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.
Rfactor
反射数
%反射
Selection details
Rfree
0.2989
543
4.8 %
RANDOM
Rwork
0.2528
-
-
-
obs
0.2551
10762
97.77 %
-
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: BABINET MODEL WITH MASK