- PDB-3hl1: CRYSTAL STRUCTURE OF A FERRITIN LIKE PROTEIN (CC_0557) FROM CAULO... -
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基本情報
登録情報
データベース: PDB / ID: 3hl1
タイトル
CRYSTAL STRUCTURE OF A FERRITIN LIKE PROTEIN (CC_0557) FROM CAULOBACTER VIBRIOIDES AT 1.95 A RESOLUTION
要素
Ferritin like protein
キーワード
METAL BINDING PROTEIN / FERRITIN-LIKE 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
0.97876
1
3
0.97828
1
反射
解像度: 1.95→29.424 Å / Num. obs: 41306 / % possible obs: 96.9 % / Observed criterion σ(I): -3 / 冗長度: 3.88 % / Biso Wilson estimate: 31.69 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 12.61
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
1.95-2.02
0.501
1.7
15357
7676
1
94.5
2.02-2.1
0.337
2.5
15676
7698
1
96.4
2.1-2.2
0.239
3.5
16811
8208
1
97.2
2.2-2.31
0.166
4.9
15145
7386
1
97.3
2.31-2.46
0.121
6.6
16794
8131
1
97.5
2.46-2.65
0.082
9.4
16128
7821
1
97.8
2.65-2.91
0.057
12.8
15929
7729
1
98
2.91-3.33
0.035
19
16358
7934
1
97.9
3.33-4.19
0.022
30.1
16068
7801
1
97
4.19-29.424
0.019
35.8
15970
7752
1
95.3
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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
autoSHARP
位相決定
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: 1.95→29.424 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.941 / Occupancy max: 1 / Occupancy min: 0.37 / SU B: 7.913 / SU ML: 0.115 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.178 / ESU R Free: 0.161 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. THE B CHAIN IS SEVERELY DISORDERED. THE MODEL FOR B CHAIN WAS BUILT BASED ON THE CHAIN A WHERE DENSITY IS NOT DEFINITE. ADDITIONALLY, A291-297 HAS POOR DENSITY. 5. AN UNKNOWN LIGAND (UNL) IS MODELED FOR EACH MONOMER IN A SITE WHERE RESIDUES ARE HIGHLY CONSERVED.
Rfactor
反射数
%反射
Selection details
Rfree
0.232
2079
5 %
RANDOM
Rwork
0.185
-
-
-
obs
0.188
41295
99.2 %
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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