- PDB-3kwr: Crystal structure of Putative RNA-binding protein (NP_785364.1) f... -
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基本情報
登録情報
データベース: PDB / ID: 3kwr
タイトル
Crystal structure of Putative RNA-binding protein (NP_785364.1) from LACTOBACILLUS PLANTARUM at 1.45 A resolution
要素
Putative RNA-binding protein
キーワード
RNA BINDING PROTEIN / Putative RNA-binding 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: Double crystal monochromator / プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長
波長: 0.97911 Å / 相対比: 1
反射
解像度: 1.45→29.67 Å / Num. obs: 40229 / % possible obs: 97 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 16.746 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 16.58
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
1.45-1.5
0.592
1.6
15319
6918
90.3
1.5-1.56
0.417
2.5
18639
7539
96.3
1.56-1.63
0.336
3.1
19394
7550
96.7
1.63-1.72
0.22
4.8
21155
7968
97.2
1.72-1.83
0.14
7.6
21186
7746
97.4
1.83-1.97
0.091
11.6
21255
7541
97.3
1.97-2.17
0.058
17.5
22190
7751
98
2.17-2.48
0.058
24.9
31341
7582
98.4
2.48-3.12
0.044
36
43910
7728
99
3.12
0.025
53.8
45405
7844
99.1
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位相決定
位相決定
手法: 単波長異常分散
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解析
ソフトウェア
名称
バージョン
分類
NB
REFMAC
5.5.0053
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
精密化
構造決定の手法: 単波長異常分散 / 解像度: 1.45→29.67 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.961 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 1.892 / SU ML: 0.033 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.054 / ESU R Free: 0.055 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 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 RECORDS CONTAIN 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.SULPHATE ANION (SO4) FROM CRYSTALLIZATION AND GLYCEROL MOLECULE (GOL) FROM CRYOPROTECTANT ARE MODELED IN THE STRUCTURE.
Rfactor
反射数
%反射
Selection details
Rfree
0.181
2017
5 %
RANDOM
Rwork
0.163
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-
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obs
0.164
40213
99.67 %
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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