Crystal structure of putative transcription regulation repressor (LACI family) FROM Corynebacterium glutamicum
要素
Transcriptional regulators
キーワード
TRANSCRIPTION REGULATOR / STRUCTURAL GENOMICS / PSI-2 / SUGAR BINDING PROTEIN / TRANSCRIPTION REGULATION / PROTEIN STRUCTURE INITIATIVE / NEW YORK SGX RESEARCH CENTER FOR STRUCTURAL GENOMICS / NYSGXRC / DNA-binding / Transcription / UNCHARACTERIZED PROTEIN
機能・相同性
機能・相同性情報
regulation of DNA-templated transcription / DNA binding 類似検索 - 分子機能
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: 0.9789 Å / 相対比: 1
反射
解像度: 2.3→40 Å / Num. obs: 32657 / % possible obs: 100 % / Observed criterion σ(I): -5 / 冗長度: 11.7 % / Biso Wilson estimate: 50.208 Å2 / Rsym value: 0.104 / Net I/σ(I): 5.1
反射 シェル
解像度: 2.3→2.38 Å / 冗長度: 11.6 % / Rmerge(I) obs: 0.95 / Mean I/σ(I) obs: 1 / % possible all: 100
-
解析
ソフトウェア
名称
バージョン
分類
SHELX
モデル構築
REFMAC
5.3.0034
精密化
HKL-2000
データ削減
HKL-2000
データスケーリング
SHELX
位相決定
精密化
構造決定の手法: 単波長異常分散 / 解像度: 2.3→20 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.913 / SU B: 7.524 / SU ML: 0.184 / 交差検証法: THROUGHOUT / ESU R: 0.265 / ESU R Free: 0.235 / 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
0.28353
1032
3.2 %
RANDOM
Rwork
0.22425
-
-
-
obs
0.22604
31506
99.91 %
-
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
原子変位パラメータ
Biso mean: 60.047 Å2
Baniso -1
Baniso -2
Baniso -3
1-
2.42 Å2
1.21 Å2
0 Å2
2-
-
2.42 Å2
0 Å2
3-
-
-
-3.62 Å2
精密化ステップ
サイクル: LAST / 解像度: 2.3→20 Å
タンパク質
核酸
リガンド
溶媒
全体
原子数
3858
0
21
74
3953
拘束条件
Refine-ID
タイプ
Dev ideal
Dev ideal target
数
X-RAY DIFFRACTION
r_bond_refined_d
0.007
0.022
3991
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.13
1.965
5439
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.239
5
525
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
37.593
24.855
173
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
15.905
15
631
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
13.896
15
20
X-RAY DIFFRACTION
r_chiral_restr
0.074
0.2
629
X-RAY DIFFRACTION
r_gen_planes_refined
0.003
0.02
3032
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
0.136
0.3
1784
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
0.292
0.5
2744
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.143
0.5
236
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
0.136
0.3
35
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.13
0.5
9
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
4.742
2
2631
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
6.77
3
4139
X-RAY DIFFRACTION
r_scbond_it
9.171
4
1500
X-RAY DIFFRACTION
r_scangle_it
12.604
6
1292
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
Refine LS restraints NCS
Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION