分子量: 4738.447 Da / 分子数: 1 / 由来タイプ: 合成 詳細: The protein was chemically synthesized. The sequence of the protein can be naturally found in Crambe abyssinica (Abyssinian crambe). 参照: UniProt: P01542
温度: 277 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7 詳細: X-ray crystallography-quality crystals for crambin-carboxamide were formed by mixing 2 ul of protein (10 mg/ml in pH 7.5 100mM HEPES buffer containing 150 mM NaCl) and 2 ul of a 0.8 M ...詳細: X-ray crystallography-quality crystals for crambin-carboxamide were formed by mixing 2 ul of protein (10 mg/ml in pH 7.5 100mM HEPES buffer containing 150 mM NaCl) and 2 ul of a 0.8 M succinic acid (used for X-ray diffraction), or by mixing 2 ul of the protein solution with 2 ul of 0.1 M HEPES buffer containing 15% v/v tacsimate and 2% w/v polyethylene glycol 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
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データ収集
放射光源
由来: シンクロトロン / サイト: APS / ビームライン: 5ID-B
放射
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
相対比: 1
反射
解像度: 1.6→20 Å / Num. all: 4566 / Num. obs: 4354
反射 シェル
解像度: 1.601→1.643 Å
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解析
ソフトウェア
名称: REFMAC / バージョン: 5.1.9999 / 分類: 精密化
精密化
構造決定の手法: 分子置換 / 解像度: 1.6→20 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.951 / SU B: 7.472 / SU ML: 0.106 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.102 / 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
0.23385
212
4.6 %
RANDOM
Rwork
0.21552
-
-
-
all
0.2165
4566
-
-
obs
0.2165
4354
97.73 %
-
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: 31.739 Å2
Baniso -1
Baniso -2
Baniso -3
1-
2.59 Å2
1.3 Å2
0 Å2
2-
-
2.59 Å2
0 Å2
3-
-
-
-3.89 Å2
精密化ステップ
サイクル: LAST / 解像度: 1.6→20 Å
タンパク質
核酸
リガンド
溶媒
全体
原子数
299
0
0
10
309
拘束条件
Refine-ID
タイプ
Dev ideal
Dev ideal target
数
X-RAY DIFFRACTION
r_bond_refined_d
0.015
0.022
308
X-RAY DIFFRACTION
r_bond_other_d
0.004
0.02
278
X-RAY DIFFRACTION
r_angle_refined_deg
1.547
1.972
425
X-RAY DIFFRACTION
r_angle_other_deg
0.964
3
650
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.117
5
42
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
26.985
22.5
8
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
15.862
15
40
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
16.58
15
2
X-RAY DIFFRACTION
r_chiral_restr
0.072
0.2
52
X-RAY DIFFRACTION
r_gen_planes_refined
0.011
0.02
340
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
54
X-RAY DIFFRACTION
r_nbd_refined
0.227
0.2
66
X-RAY DIFFRACTION
r_nbd_other
0.198
0.2
253
X-RAY DIFFRACTION
r_nbtor_refined
X-RAY DIFFRACTION
r_nbtor_other
0.087
0.2
169
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.146
0.2
2
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
0.137
0.2
7
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.155
0.2
39
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.327
0.2
10
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
1.101
1.5
278
X-RAY DIFFRACTION
r_mcbond_other
0.216
1.5
87
X-RAY DIFFRACTION
r_mcangle_it
1.42
2
350
X-RAY DIFFRACTION
r_scbond_it
2.306
3
107
X-RAY DIFFRACTION
r_scangle_it
2.922
4.5
75
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: 1.601→1.643 Å / Total num. of bins used: 20 /
Rfactor
反射数
Rfree
0.332
12
Rwork
0.295
279
精密化 TLS
手法: refined / Origin x: 0.9386 Å / Origin y: 17.8807 Å / Origin z: 4.9781 Å