- PDB-5o5e: Crystal structure of human UDP-N-acetylglucosamine-dolichyl-phosp... -
+
データを開く
IDまたはキーワード:
読み込み中...
-
基本情報
登録情報
データベース: PDB / ID: 5o5e
タイトル
Crystal structure of human UDP-N-acetylglucosamine-dolichyl-phosphate N-acetylglucosaminephosphotransferase (DPAGT1) (V264G mutant) in complex with tunicamycin
構造決定の手法: 分子置換 / 解像度: 3.4→25.87 Å / Cor.coef. Fo:Fc: 0.9076 / Cor.coef. Fo:Fc free: 0.9298 / 交差検証法: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.428 詳細: STRUCTURE REFINED WITH BUSTER WITH A SINGLE TLS GROUP. ELECTRON DENSITY MAPS WERE SHARPENED WITH -100A**2 BFACTOR FOR REBUILDING IN COOT.
Rfactor
反射数
%反射
Selection details
Rfree
0.2363
552
5.12 %
RANDOM
Rwork
0.2294
-
-
-
obs
0.2298
10786
99.9 %
-
原子変位パラメータ
Biso mean: 172.25 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-5.492 Å2
0 Å2
0 Å2
2-
-
-5.492 Å2
0 Å2
3-
-
-
10.9839 Å2
Refine analyze
Luzzati coordinate error obs: 0.439 Å
精密化ステップ
サイクル: 1 / 解像度: 3.4→25.87 Å
タンパク質
核酸
リガンド
溶媒
全体
原子数
2937
0
104
9
3050
拘束条件
Refine-ID
タイプ
Dev ideal
数
Restraint function
Weight
X-RAY DIFFRACTION
t_bond_d
0.009
3117
HARMONIC
2
X-RAY DIFFRACTION
t_angle_deg
1
4238
HARMONIC
2
X-RAY DIFFRACTION
t_dihedral_angle_d
1399
SINUSOIDAL
2
X-RAY DIFFRACTION
t_incorr_chiral_ct
X-RAY DIFFRACTION
t_pseud_angle
X-RAY DIFFRACTION
t_trig_c_planes
43
HARMONIC
2
X-RAY DIFFRACTION
t_gen_planes
451
HARMONIC
5
X-RAY DIFFRACTION
t_it
3117
HARMONIC
20
X-RAY DIFFRACTION
t_nbd
X-RAY DIFFRACTION
t_omega_torsion
2.22
X-RAY DIFFRACTION
t_other_torsion
3.1
X-RAY DIFFRACTION
t_improper_torsion
X-RAY DIFFRACTION
t_chiral_improper_torsion
424
SEMIHARMONIC
5
X-RAY DIFFRACTION
t_sum_occupancies
X-RAY DIFFRACTION
t_utility_distance
X-RAY DIFFRACTION
t_utility_angle
X-RAY DIFFRACTION
t_utility_torsion
X-RAY DIFFRACTION
t_ideal_dist_contact
3888
SEMIHARMONIC
4
LS精密化 シェル
解像度: 3.4→3.8 Å / Total num. of bins used: 5
Rfactor
反射数
%反射
Rfree
0.2602
147
4.94 %
Rwork
0.2095
2826
-
all
0.2118
2973
-
obs
-
-
99.97 %
精密化 TLS
手法: refined / Origin x: 45.6838 Å / Origin y: 49.8451 Å / Origin z: 128.728 Å