- PDB-3h50: CRYSTAL STRUCTURE OF A TETRACENOMYCIN POLYKETIDE SYNTHESIS PROTEI... -
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基本情報
登録情報
データベース: PDB / ID: 3h50
タイトル
CRYSTAL STRUCTURE OF A TETRACENOMYCIN POLYKETIDE SYNTHESIS PROTEIN (TCMJ) FROM XANTHOMONAS CAMPESTRIS PV. CAMPESTRIS AT 1.60 A RESOLUTION
要素
Tetracenomycin polyketide synthesis protein
キーワード
BIOSYNTHETIC PROTEIN / TETRACENOMYCIN POLYKETIDE SYNTHESIS PROTEIN / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...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
モノクロメーター: Single crystal Si(111) bent monochromator (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
0.979616
1
3
0.979305
1
反射
解像度: 1.6→28.502 Å / Num. obs: 13913 / % possible obs: 96.8 % / Observed criterion σ(I): -3 / 冗長度: 7.2 % / Biso Wilson estimate: 11.422 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 9.99
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
1.59-1.65
0.61
1.9
8850
2430
1
80.3
1.65-1.71
0.535
2.3
9471
2496
1
98.6
1.71-1.79
0.424
3
10553
2860
1
98.6
1.79-1.88
0.341
3.8
10112
2689
1
98.9
1.88-2
0.233
5.7
9653
2816
1
98
2-2.16
0.167
7.9
10465
2905
1
98.7
2.16-2.37
0.123
10.4
9838
2696
1
99.3
2.37-2.72
0.096
12.7
10648
2904
1
99.1
2.72-3.42
0.055
20.6
10213
2742
1
99.4
3.42-28.502
0.034
29.8
10350
2813
1
98.4
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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
5.2.0019
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
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: 1.6→28.502 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.932 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.667 / SU ML: 0.074 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.1 / ESU R Free: 0.1 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). ZINC WAS MODELED IN FOUR SITES THAT COINCIDE WITH PEAKS IN THE ANOMALOUS DIFFERENCE ...詳細: 1). HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2). ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY 3). ZINC WAS MODELED IN FOUR SITES THAT COINCIDE WITH PEAKS IN THE ANOMALOUS DIFFERENCE FOURIER. X-RAY FLUORESCENCE MEASUREMENTS CONFIRM THAT ZINC IS PRESENT AND NICKEL IS ABSENT FROM THE SAMPLE. 4). ACETATE MOLECULES FROM THE CRYSTALLIZATION SOLUTIONS HAVE BEEN MODELED INTO THE STRUCTURE. 5). UNEXPLAINED ELECTRON DENSITIES WERE OBSERVED WITHIN COORDINATION DISTANCE OF ZN 2, ZN 3, AND ZN 4. LIGANDS WERE NOT MODELED INTO THESE ELECTRON DENSITIES.
Rfactor
反射数
%反射
Selection details
Rfree
0.22
696
5 %
RANDOM
Rwork
0.182
-
-
-
obs
0.184
13912
98.9 %
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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: BABINET MODEL WITH MASK