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: 2.37 Å3/Da / 溶媒含有率: 48 % 解説: THE RMERGE AND STATISTICS REPORTED HERE BY XSCALE ARE BASED ON TREATING FRIEDEL PAIRS AS SEPARATE REFLECTIONS.
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: 9 詳細: 3.2M ammonium sulfate, 0.1M Bicine pH 9.0, Additive: 0.001 M acetyl Co-enzyme A, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
モノクロメーター: Single crystal Si(311) bent monochromator (horizontal focusing) 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: 0.979032 Å / 相対比: 1
反射
解像度: 1.52→27.146 Å / Num. obs: 25437 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / 冗長度: 3.97 % / Biso Wilson estimate: 15.026 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 12.44
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
1.52-1.57
0.443
2.1
9028
4403
1
98.3
1.57-1.64
0.341
2.7
11114
5366
1
99.1
1.64-1.71
0.25
3.7
9422
4517
1
99.3
1.71-1.8
0.185
4.9
10104
4838
1
99.1
1.8-1.91
0.128
7.1
9838
4705
1
99
1.91-2.06
0.08
10.4
10367
4924
1
98.8
2.06-2.27
0.052
15.3
10262
4862
1
99.2
2.27-2.6
0.039
19.2
10227
4828
1
98.8
2.6-3.27
0.03
24.5
10046
4739
1
98
3.27-27.146
0.019
34.4
10227
4791
1
98
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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
5.2.0005
精密化
PHENIX
精密化
SOLVE
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
精密化
構造決定の手法: 単波長異常分散 / 解像度: 1.52→27.146 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.962 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 2.247 / SU ML: 0.044 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.07 / ESU R Free: 0.067 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. TLS GROUPS WERE ASSIGNED WITH THE AID OF THE TLSMD SERVER. 5. ACETYL COENZYME A WAS INCLUDED AS AN ADDITIVE FOR CRYSTALLIZATION. WE SEE NO DENSITY FOR THE ACETYL GROUP AND HAVE MODELED IT IN THE STRUCTURE AS COENZYME A. THE PANTHOTHENATE AND BETA-MERCAPTOETHYLAMINE MOIETIES OF THE CO-A ARE DISORDERED AND HAVE BEEN MODELED IN TWO CONFORMATIONS. THE PEPTIDE LINKING THE PANTHOTHENATE AND BETA-MERCAPTOETHYLAMINE IN CONFORMER A HAS BEEN BUILT IN A DIFFERENT ORIENTATION THAT IN THE MODEL FOR THE RELATED PH 6 STRUCTURE. WHILE THIS APPEARS PLAUSIBLE, GIVEN THE AMBIGUITY IN THE DENSITY FOR THIS REGION, NO CONCLUSIONS SHOULD BE DRAWN WITH HIGH CONFIDENCE. 6. FOUR SULFATE IONS AND TWO GLYCEROL MOLECULES FROM THE CRYSTALLIZATION AND CRYOPROTECTION CONDITIONS HAVE BEEN MODELED IN THE STRUCTURE. ONE OF THE SULFATE MOLECULES, A204, WAS MODELED WITH PARTIAL OCCUPANCY IN TWO ALTERNATE POSITIONS AT THE PUTATIVE ACTIVE SITE. ASSIGNMENT OF THIS ELECTRON DENSITY TO A DISORDERED SULFATE IS TENTATIVE. 7. LOOPS 131-134 and 70-73 ARE DISORDERED.
Rfactor
反射数
%反射
Selection details
Rfree
0.178
1301
5.1 %
RANDOM
Rwork
0.16
-
-
-
obs
0.161
25434
99.74 %
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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