- PDB-3but: Crystal structure of protein Af_0446 from Archaeoglobus fulgidus -
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基本情報
登録情報
データベース: PDB / ID: 3but
タイトル
Crystal structure of protein Af_0446 from Archaeoglobus fulgidus
要素
Uncharacterized protein Af_0446
キーワード
STRUCTURAL GENOMICS / UNKNOWN FUNCTION / LIPID BINDING PROTEIN / BETA BARREL / PROTEIN STRUCTURE INITIATIVE / PSI-2 / New York SGX Research Center for Structural Genomics / NYSGXRC
モノクロメーター: Diamond / 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: 0.9796 Å / 相対比: 1
反射
解像度: 1.9→50 Å / Num. obs: 9264 / % possible obs: 99.6 % / Observed criterion σ(I): -0.5 / 冗長度: 7.5 % / Biso Wilson estimate: 34.66 Å2 / Rmerge(I) obs: 0.142 / Net I/σ(I): 4.4
反射 シェル
解像度: 1.9→1.97 Å / 冗長度: 3.4 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 0.8 / % possible all: 97.1
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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
MAR345
CCD
データ収集
HKL-2000
データ削減
HKL-2000
データスケーリング
SHELXD
位相決定
精密化
構造決定の手法: 単波長異常分散 / 解像度: 1.91→20 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.916 / SU B: 12.517 / SU ML: 0.162 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / ESU R: 0.278 / ESU R Free: 0.236 / 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. ANISOTROPY CORRECTION WAS APPLIED TO DIFFRACTION DATA. 3. UNDEFINED LIGAND OR COFACTOR IS BOUND INTO THE CENTRAL CAVITY, A PART OF IT ...詳細: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ANISOTROPY CORRECTION WAS APPLIED TO DIFFRACTION DATA. 3. UNDEFINED LIGAND OR COFACTOR IS BOUND INTO THE CENTRAL CAVITY, A PART OF IT IS MOST LIKELY A LIPID. THIS LIGAND HAS NOT BEEN MODELED.
Rfactor
反射数
%反射
Selection details
Rfree
0.29963
231
3 %
RANDOM
Rwork
0.22606
-
-
-
obs
0.22816
7375
83.01 %
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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: 1.5 Å / 溶媒モデル: MASK
原子変位パラメータ
Biso mean: 28.881 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.55 Å2
0 Å2
0 Å2
2-
-
-0.16 Å2
0 Å2
3-
-
-
-0.4 Å2
精密化ステップ
サイクル: LAST / 解像度: 1.91→20 Å
タンパク質
核酸
リガンド
溶媒
全体
原子数
985
0
0
50
1035
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
1064
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.122
1.959
1454
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.489
5
140
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
36.76
24.091
44
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
17.893
15
203
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
25.339
15
7
X-RAY DIFFRACTION
r_chiral_restr
0.074
0.2
174
X-RAY DIFFRACTION
r_gen_planes_refined
0.003
0.02
777
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
0.127
0.3
363
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
0.299
0.5
701
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.145
0.5
99
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
0.104
0.3
64
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.159
0.5
19
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
5.398
2.5
669
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
6.871
3
1073
X-RAY DIFFRACTION
r_scbond_it
10.757
3.5
449
X-RAY DIFFRACTION
r_scangle_it
14.8
5
372
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: 1.91→1.96 Å / Total num. of bins used: 20
Rfactor
反射数
%反射
Rfree
0.36
3
-
Rwork
0.287
107
-
obs
-
-
16.52 %
精密化 TLS
手法: refined / Origin x: -17.638 Å / Origin y: 7.91 Å / Origin z: -8.006 Å