IX/X-BP IS A DISULFIDE-LINKED HETERODIMER PROTEIN CONSISTING OF HOMOLOGOUS SUBUNITS. EACH SUBUNIT ...IX/X-BP IS A DISULFIDE-LINKED HETERODIMER PROTEIN CONSISTING OF HOMOLOGOUS SUBUNITS. EACH SUBUNIT IS HOMOLOGOUS TO THE CARBOHYDRATE-RECOGNITION DOMAIN OF C-TYPE LECTIN, AND IX/X-BP BELONGS TO THE C-TYPE LECTIN SUPERFAMILY.
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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: 2
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試料調製
結晶
マシュー密度: 3 Å3/Da / 溶媒含有率: 59 %
結晶化
pH: 7.8 詳細: 60% SATURATED AMMONIUM SULFATE, 20 MM TRIS-HCL, 3 MM CACL2, PH 7.8
解像度: 2.5→50 Å / Num. obs: 29883 / % possible obs: 87 % / Observed criterion σ(I): 1 / 冗長度: 3.8 % / Biso Wilson estimate: 30.6 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 39
反射 シェル
解像度: 2.5→2.61 Å / Rmerge(I) obs: 0.229 / Mean I/σ(I) obs: 6 / % possible all: 75
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解析
ソフトウェア
名称
バージョン
分類
DENZO
データ削減
SCALEPACK
データスケーリング
X-PLOR
3.1
モデル構築
X-PLOR
3.1
精密化
X-PLOR
3.1
位相決定
精密化
構造決定の手法: 単一同系置換・異常分散 / 解像度: 2.5→6 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2000000 / Data cutoff low absF: 0.001 / 交差検証法: THROUGHOUT / σ(F): 2 詳細: PARAMETER AND TOPOLOGY FILES FOR SOLVENT WERE PREPARED FROM TUTORIAL FILES IN THE X-PLOR MANUAL.
Rfactor
反射数
%反射
Selection details
Rfree
0.221
1228
5 %
RANDOM
Rwork
0.178
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obs
0.178
25211
80 %
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原子変位パラメータ
Biso mean: 29.2 Å2
Refine analyze
Free
Obs
Luzzati coordinate error
0.33 Å
0.25 Å
Luzzati d res low
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6 Å
Luzzati sigma a
0.41 Å
0.33 Å
精密化ステップ
サイクル: LAST / 解像度: 2.5→6 Å
タンパク質
核酸
リガンド
溶媒
全体
原子数
6177
0
6
146
6329
拘束条件
Refine-ID
タイプ
Dev ideal
Dev ideal target
X-RAY DIFFRACTION
x_bond_d
0.007
X-RAY DIFFRACTION
x_bond_d_na
X-RAY DIFFRACTION
x_bond_d_prot
X-RAY DIFFRACTION
x_angle_d
X-RAY DIFFRACTION
x_angle_d_na
X-RAY DIFFRACTION
x_angle_d_prot
X-RAY DIFFRACTION
x_angle_deg
1.5
X-RAY DIFFRACTION
x_angle_deg_na
X-RAY DIFFRACTION
x_angle_deg_prot
X-RAY DIFFRACTION
x_dihedral_angle_d
24.5
X-RAY DIFFRACTION
x_dihedral_angle_d_na
X-RAY DIFFRACTION
x_dihedral_angle_d_prot
X-RAY DIFFRACTION
x_improper_angle_d
1.19
X-RAY DIFFRACTION
x_improper_angle_d_na
X-RAY DIFFRACTION
x_improper_angle_d_prot
X-RAY DIFFRACTION
x_mcbond_it
4.29
1.5
X-RAY DIFFRACTION
x_mcangle_it
6.3
2
X-RAY DIFFRACTION
x_scbond_it
6.41
2
X-RAY DIFFRACTION
x_scangle_it
8.69
2.5
LS精密化 シェル
解像度: 2.5→2.64 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6