positive regulation of chromatin binding / histone H3K9me2/H3K9me3 demethylase activity / [histone H3]-trimethyl-L-lysine9 demethylase / positive regulation of double-strand break repair via nonhomologous end joining / histone H3K9 demethylase activity / histone demethylase activity / pericentric heterochromatin / cellular response to ionizing radiation / regulation of protein phosphorylation / double-strand break repair via homologous recombination ...positive regulation of chromatin binding / histone H3K9me2/H3K9me3 demethylase activity / [histone H3]-trimethyl-L-lysine9 demethylase / positive regulation of double-strand break repair via nonhomologous end joining / histone H3K9 demethylase activity / histone demethylase activity / pericentric heterochromatin / cellular response to ionizing radiation / regulation of protein phosphorylation / double-strand break repair via homologous recombination / HDMs demethylate histones / chromatin DNA binding / site of double-strand break / 遺伝子発現の調節 / damaged DNA binding / blood microparticle / クロマチンリモデリング / 炎症 / クロマチン / 核質 / metal ion binding / 細胞核 類似検索 - 分子機能
JmjN domain / jmjN domain / JmjN domain profile. / Small domain found in the jumonji family of transcription factors / Cupin / JmjC domain, hydroxylase / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Jelly Rolls ...JmjN domain / jmjN domain / JmjN domain profile. / Small domain found in the jumonji family of transcription factors / Cupin / JmjC domain, hydroxylase / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Jelly Rolls / サンドイッチ / Mainly Beta 類似検索 - ドメイン・相同性
LYSINE-SPECIFICDEMETHYLASE4D / JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN 3D / JU MONJI DOMAIN-CONTAINING PROTEIN 2D / ...JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN 3D / JU MONJI DOMAIN-CONTAINING PROTEIN 2D / HUMAN LYSINE-SPECIFIC DEMETHYL ASE 4D / JMJD2D
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: 1.54178 Å / 相対比: 1
反射
解像度: 1.91→41.86 Å / Num. obs: 30844 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / 冗長度: 4.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 18.8
反射 シェル
解像度: 1.91→2.01 Å / 冗長度: 3.9 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 3.9 / % possible all: 99.8
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解析
ソフトウェア
名称
バージョン
分類
REFMAC
5.8.0073
精密化
XDS
データ削減
SCALA
データスケーリング
精密化
構造決定の手法: 分子置換 開始モデル: NONE 解像度: 1.91→31.15 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.936 / SU B: 5.879 / SU ML: 0.089 / 交差検証法: THROUGHOUT / ESU R: 0.141 / ESU R Free: 0.133 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD / 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
Rfactor
反射数
%反射
Selection details
Rfree
0.20319
1550
5 %
RANDOM
Rwork
0.16035
-
-
-
obs
0.16243
29158
99.3 %
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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