Crystal structure of sugar ABC transporter (sugar-binding protein) from Bacillus halodurans
要素
Sugar ABC transporter
キーワード
TRANSPORT PROTEIN / Sugar ABC transporter / Sugar-binding protein / Bacillus halodurans / target 11229f / Structural Genomics / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
解像度: 2.02→2.05 Å / 冗長度: 2.1 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.1 / % possible all: 88.4
-
解析
ソフトウェア
名称
バージョン
分類
CBASS
データ収集
PHENIX
モデル構築
REFMAC
5.2.0019
精密化
HKL-2000
データ削減
HKL-2000
データスケーリング
PHENIX
位相決定
精密化
構造決定の手法: 単波長異常分散 / 解像度: 2.02→33.92 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.924 / SU B: 9.949 / SU ML: 0.133 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.227 / ESU R Free: 0.183 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD 詳細: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. Residues listed as missing in Remark 465 are due to lack of electron density. Residues with missing atoms listed in Remark 470 are due ...詳細: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. Residues listed as missing in Remark 465 are due to lack of electron density. Residues with missing atoms listed in Remark 470 are due to lack of electron density for side chains and modeled as alanines. Program Phenix.refine has also been used in refinement.
Rfactor
反射数
%反射
Selection details
Rfree
0.23711
1760
5 %
RANDOM
Rwork
0.19308
-
-
-
obs
0.19527
33281
100 %
-
all
-
33281
-
-
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: 31.04 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.46 Å2
0 Å2
0 Å2
2-
-
0.48 Å2
0 Å2
3-
-
-
-0.02 Å2
精密化ステップ
サイクル: LAST / 解像度: 2.02→33.92 Å
タンパク質
核酸
リガンド
溶媒
全体
原子数
4470
0
0
229
4699
拘束条件
Refine-ID
タイプ
Dev ideal
Dev ideal target
数
X-RAY DIFFRACTION
r_bond_refined_d
0.021
0.022
4558
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.805
1.947
6210
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
7.232
5
578
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
35.526
25.516
223
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
16.739
15
712
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
16.387
15
17
X-RAY DIFFRACTION
r_chiral_restr
0.122
0.2
704
X-RAY DIFFRACTION
r_gen_planes_refined
0.008
0.02
3527
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
0.218
0.2
2184
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
0.313
0.2
3170
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.17
0.2
269
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
0.214
0.2
28
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.188
0.2
17
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
1.315
1.5
2955
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
1.849
2
4607
X-RAY DIFFRACTION
r_scbond_it
3.315
3
1835
X-RAY DIFFRACTION
r_scangle_it
4.759
4.5
1603
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: 2.02→2.08 Å / Total num. of bins used: 20
Rfactor
反射数
%反射
Rfree
0.329
93
-
Rwork
0.247
1568
-
obs
-
-
100 %
精密化 TLS
手法: refined / Origin x: 34.321 Å / Origin y: 42.02 Å / Origin z: 54.056 Å