- PDB-3f14: Crystal structure of NTF2-like protein of unknown function (YP_68... -
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基本情報
登録情報
データベース: PDB / ID: 3f14
タイトル
Crystal structure of NTF2-like protein of unknown function (YP_680363.1) from CYTOPHAGA HUTCHINSONII ATCC 33406 at 1.45 A resolution
要素
uncharacterized NTF2-like protein
キーワード
structural genomics / unknown function / YP_680363.1 / NTF2-like protein of unknown function / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
機能・相同性
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 / TRIETHYLENE GLYCOL / SnoaL-like domain-containing protein
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.
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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: 1
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試料調製
結晶
マシュー密度: 2.21 Å3/Da / 溶媒含有率: 44.39 %
結晶化
温度: 277 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 8.5 詳細: 0.2000M NaOAc, 30.0000% PEG-4000, 0.1M TRIS pH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
解像度: 1.45→25.933 Å / Num. obs: 20633 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / 冗長度: 7.16 % / Biso Wilson estimate: 17.008 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 16.58
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
1.45-1.5
0.538
2.5
13549
3671
1
98.8
1.5-1.56
0.377
3.6
14859
3965
1
99.8
1.56-1.63
0.266
5
14450
3839
1
99.8
1.63-1.72
0.187
6.9
15535
4101
1
99.8
1.72-1.83
0.132
9.6
15078
3971
1
99.9
1.83-1.97
0.082
14.5
14858
3907
1
99.9
1.97-2.17
0.054
21.7
14853
3892
1
99.8
2.17-2.48
0.041
26.6
14744
3850
1
99.7
2.48-3.12
0.032
33.5
14887
3872
1
99.6
3.12-25.933
0.025
41.8
14983
3931
1
99.4
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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: 1.45→25.933 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.968 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 2.333 / SU ML: 0.045 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.069 / ESU R Free: 0.064 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4.PEG MOLECULE AND TRIS ANION FROM CRYSTALLIZATION ARE MODELED INTO THIS STRUCTURE.
Rfactor
反射数
%反射
Selection details
Rfree
0.181
1054
5.1 %
RANDOM
Rwork
0.171
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obs
0.171
20606
99.85 %
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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