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 / regulation of gene expression / blood microparticle / damaged DNA binding / inflammatory response / chromatin remodeling / chromatin / nucleoplasm / nucleus / metal ion binding 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 / Sandwich / Mainly Beta 類似検索 - ドメイン・相同性
NICKEL (II) ION / N-OXALYLGLYCINE / Lysine-specific demethylase 4D 類似検索 - 構成要素
PanDDA analysis group deposition of models of ground state datasets
タイプ
ground state
解説
Jmjc domain of human JMJD2D screened against the ZENOBIA Fragment Library by X-ray Crystallography. Check out the PanDDA event maps at https://zenodo.org/record/290220/files/0_index.html
解像度: 1.27→29.34 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.967 / SU B: 0.662 / SU ML: 0.028 / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.044 / ESU R Free: 0.046 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
Rfactor
反射数
%反射
Selection details
Rfree
0.1774
4612
4.9 %
RANDOM
Rwork
0.1585
-
-
-
obs
0.1594
89616
91.69 %
-
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