- PDB-3dxo: CRYSTAL STRUCTURE OF A PUTATIVE ISOMERASE OF THE SNOAL-LIKE FAMIL... -
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基本情報
登録情報
データベース: PDB / ID: 3dxo
タイトル
CRYSTAL STRUCTURE OF A PUTATIVE ISOMERASE OF THE SNOAL-LIKE FAMILY (ATU_0744) FROM AGROBACTERIUM TUMEFACIENS STR. C58 AT 2.70 A RESOLUTION
要素
uncharacterized SnoaL-like Protein
キーワード
ISOMERASE / PUTATIVE ISOMERASE OF THE SNOAL-LIKE FAMILY / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
機能・相同性
機能・相同性情報
SnoaL-like domain / SnoaL-like domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta 類似検索 - ドメイン・相同性
AUTHORS STATE THAT THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAINS THAT FORM A DIMER BASED ON CRYSTAL PACKING ANALYSIS.
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.
解像度: 2.7→28.724 Å / Num. obs: 11229 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 49.301 Å2 / Rmerge(I) obs: 0.113 / Net I/σ(I): 7.04
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
2.7-2.8
0.454
1.9
4048
2098
97.8
2.8-2.91
0.363
2.3
3899
2006
98.8
2.91-3.04
0.288
3.1
3940
2029
99.1
3.04-3.2
0.213
4.1
3936
2041
98.5
3.2-3.4
0.146
5.7
3947
2038
98.8
3.4-3.66
0.104
7.9
3963
2038
99.1
3.66-4.03
0.085
9.5
4031
2073
99
4.03-4.6
0.065
11.8
3980
2037
98.8
4.6-5.77
0.064
11.3
3921
1970
96.1
5.77
0.048
13.2
4076
1961
90.8
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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
3.004
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: 2.7→28.724 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.885 / SU B: 23.031 / SU ML: 0.232 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.515 / ESU R Free: 0.307 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. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...詳細: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. 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. 4. PEG FRAGMENTS (PEG AND PGE) FROM THE PEG6000 AND PEG200 PRESENT IN THE CRYSTALLIZATION AND CRYOPROTECTION CONDITIONS HAVE BEEN MODELED IN THE SOLVENT STRUCTURE.
Rfactor
反射数
%反射
Selection details
Rfree
0.262
542
4.8 %
RANDOM
Rwork
0.231
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-
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obs
0.233
11216
98.41 %
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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