ジャーナル: J.Biol.Chem. / 年: 2006 タイトル: Further insight into S-adenosylmethionine-dependent methyltransferases: structural characterization of Hma, an enzyme essential for the biosynthesis of oxygenated mycolic acids in ...タイトル: Further insight into S-adenosylmethionine-dependent methyltransferases: structural characterization of Hma, an enzyme essential for the biosynthesis of oxygenated mycolic acids in Mycobacterium tuberculosis. 著者: Boissier, F. / Bardou, F. / Guillet, V. / Uttenweiler-Joseph, S. / Daffe, M. / Quemard, A. / Mourey, L.
履歴
登録
2006年1月4日
登録サイト: RCSB / 処理サイト: RCSB
改定 1.0
2006年1月17日
Provider: repository / タイプ: Initial release
改定 1.1
2008年5月1日
Group: Version format compliance
改定 1.2
2011年7月13日
Group: Advisory / Source and taxonomy / Version format compliance
解像度: 2→30 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.921 / SU B: 6.911 / SU ML: 0.099 / TLS residual ADP flag: LIKELY RESIDUAL Isotropic thermal model: isotropic + anisotropic in the last stages of refinement (TLS parameters were refined using a single group) 交差検証法: THROUGHOUT / ESU R: 0.15 / ESU R Free: 0.155 / 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
0.23889
1302
5.1 %
RANDOM
Rwork
0.17928
-
-
-
all
0.18214
24184
-
-
obs
0.18214
24184
97.5 %
-
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
原子変位パラメータ
Biso mean: 36.975 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.52 Å2
0.26 Å2
0 Å2
2-
-
0.52 Å2
0 Å2
3-
-
-
-0.78 Å2
精密化ステップ
サイクル: LAST / 解像度: 2→30 Å
タンパク質
核酸
リガンド
溶媒
全体
原子数
2236
0
27
153
2416
拘束条件
Refine-ID
タイプ
Dev ideal
Dev ideal target
数
X-RAY DIFFRACTION
r_bond_refined_d
0.016
0.022
2319
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.539
1.965
3146
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.55
5
280
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
33.269
23.54
113
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
13.197
15
376
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
21.181
15
17
X-RAY DIFFRACTION
r_chiral_restr
0.114
0.2
341
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.02
1787
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
0.201
0.2
1063
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
0.31
0.2
1590
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.17
0.2
136
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.183
0.2
21
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.202
0.2
6
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
0.975
1.5
1454
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
1.489
2
2263
X-RAY DIFFRACTION
r_scbond_it
2.566
3
1000
X-RAY DIFFRACTION
r_scangle_it
3.916
4.5
883
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS精密化 シェル
解像度: 2→2.052 Å / Total num. of bins used: 20
Rfactor
反射数
%反射
Rfree
0.304
93
-
Rwork
0.201
1482
-
obs
-
-
83.07 %
精密化 TLS
手法: refined / Origin x: 24.1462 Å / Origin y: -4.9533 Å / Origin z: 16.7397 Å