- PDB-3qkb: Crystal structure of a Protein with unknown function which belong... -
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IDまたはキーワード:
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基本情報
登録情報
データベース: PDB / ID: 3qkb
タイトル
Crystal structure of a Protein with unknown function which belongs to Pfam DUF74 family (PEPE_0654) from Pediococcus pentosaceus ATCC 25745 at 2.73 A resolution
要素
Uncharacterized protein
キーワード
Structural Genomics / Unknown function / BETA/ALPHA-PROPELLER / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY
機能・相同性
UPF0145 domain superfamily / Hypothetical protein apc22750. Chain B / Translation Initiation Factor IF3 / 2-Layer Sandwich / Alpha Beta / Uncharacterized protein
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
0.91162
1
2
0.97929
1
反射
解像度: 2.73→47.727 Å / Num. obs: 17422 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 60.247 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.92
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
2.73-2.83
0.757
2.1
6530
1768
1
99.3
2.83-2.94
0.516
2.9
6146
1667
1
99.3
2.94-3.07
0.408
3.5
6148
1674
1
99.3
3.07-3.23
0.272
5.1
6292
1707
1
99.1
3.23-3.44
0.185
7.1
6556
1782
1
99.3
3.44-3.7
0.135
9.3
6245
1704
1
99.1
3.7-4.07
0.086
13.5
6317
1737
1
99.3
4.07-4.65
0.054
18.8
6309
1738
1
99.1
4.65-5.84
0.05
20.5
6423
1781
1
98.7
5.84-47.727
0.044
24.8
6490
1864
1
95.7
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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
MolProbity
3beta29
モデル構築
PDB_EXTRACT
3.1
データ抽出
SHELX
位相決定
SHARP
位相決定
XSCALE
データスケーリング
REFMAC
5.5.0110
精密化
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: 2.73→47.727 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.916 / Occupancy max: 1 / Occupancy min: 0.37 / SU B: 24.741 / SU ML: 0.238 / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.782 / ESU R Free: 0.314 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 RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT.
Rfactor
反射数
%反射
Selection details
Rfree
0.2393
884
5.1 %
RANDOM
Rwork
0.2018
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-
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obs
0.2037
17408
98.95 %
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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: 1.4 Å / 溶媒モデル: MASK