- PDB-2qyz: Crystal structure of the uncharacterized protein CTC02137 from Cl... -
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基本情報
登録情報
データベース: PDB / ID: 2qyz
タイトル
Crystal structure of the uncharacterized protein CTC02137 from Clostridium tetani E88
要素
Uncharacterized protein
キーワード
STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Clostridium tetani E88 / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
機能・相同性
機能・相同性情報
ctc02137 like domains / YopX-like domains / Conserved hypothetical protein CHP1671 / YopX-like, C-terminal / YopX protein / YopX protein / Dna Ligase; domain 1 / SH3 type barrels. / Roll / 2-Layer Sandwich ...ctc02137 like domains / YopX-like domains / Conserved hypothetical protein CHP1671 / YopX-like, C-terminal / YopX protein / YopX protein / Dna Ligase; domain 1 / SH3 type barrels. / Roll / 2-Layer Sandwich / Mainly Beta / Alpha Beta 類似検索 - ドメイン・相同性
YopX protein domain-containing protein 類似検索 - 構成要素
BIOMOLECULE: 1 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION ... BIOMOLECULE: 1 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON BURIED SURFACE AREA. THE DIMER IS DISULFIDE-LINKED THROUGH CYS-92.
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: 0.979 Å / 相対比: 1
Reflection
冗長度: 4.9 % / Av σ(I) over netI: 18.3 / 数: 81550 / Rmerge(I) obs: 0.035 / Χ2: 1.14 / D res high: 2.04 Å / D res low: 50 Å / Num. obs: 16582 / % possible obs: 89.3
Diffraction reflection shell
最高解像度 (Å)
最低解像度 (Å)
% possible obs (%)
ID
Rmerge(I) obs
Chi squared
Redundancy
4.39
50
96.3
1
0.024
1.784
5.3
3.49
4.39
96.6
1
0.036
2.088
5.3
3.05
3.49
100
1
0.036
1.244
5.7
2.77
3.05
100
1
0.048
0.992
5.7
2.57
2.77
99.9
1
0.063
0.809
5.7
2.42
2.57
100
1
0.09
0.681
5.5
2.3
2.42
98.9
1
0.109
0.618
4.7
2.2
2.3
89.3
1
0.196
1.369
3.5
2.11
2.2
71.6
1
0.172
0.523
3
2.04
2.11
39.6
1
0.183
0.509
2.6
反射
解像度: 2.04→50 Å / Num. obs: 16582 / % possible obs: 89.3 % / 冗長度: 4.9 % / Rmerge(I) obs: 0.035 / Χ2: 1.143 / Net I/σ(I): 18.3
反射 シェル
解像度 (Å)
冗長度 (%)
Rmerge(I) obs
Num. unique all
Χ2
Diffraction-ID
% possible all
2.04-2.11
2.6
0.183
722
0.509
1
39.6
2.11-2.2
3
0.172
1326
0.523
1
71.6
2.2-2.3
3.5
0.196
1656
1.369
1
89.3
2.3-2.42
4.7
0.109
1847
0.618
1
98.9
2.42-2.57
5.5
0.09
1866
0.681
1
100
2.57-2.77
5.7
0.063
1834
0.809
1
99.9
2.77-3.05
5.7
0.048
1848
0.992
1
100
3.05-3.49
5.7
0.036
1872
1.244
1
100
3.49-4.39
5.3
0.036
1796
2.088
1
96.6
4.39-50
5.3
0.024
1815
1.784
1
96.3
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解析
ソフトウェア
名称
バージョン
分類
NB
DENZO
データ削減
SCALEPACK
データスケーリング
REFMAC
精密化
PDB_EXTRACT
3
データ抽出
CBASS
データ収集
SHELXS
位相決定
精密化
解像度: 2.04→19.7 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.938 / SU B: 22.616 / SU ML: 0.242 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.212 / ESU R Free: 0.199 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD 詳細: The Bijvoet differences were used for phasing. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
反射数
%反射
Selection details
Rfree
0.259
435
4.8 %
RANDOM
Rwork
0.191
-
-
-
obs
0.194
9007
92.09 %
-
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: 54.382 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.21 Å2
0.1 Å2
0 Å2
2-
-
0.21 Å2
0 Å2
3-
-
-
-0.31 Å2
精密化ステップ
サイクル: LAST / 解像度: 2.04→19.7 Å
タンパク質
核酸
リガンド
溶媒
全体
原子数
1044
0
0
67
1111
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
1066
X-RAY DIFFRACTION
r_angle_refined_deg
2.008
1.956
1438
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
8.538
5
128
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
42.195
25.614
57
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
19.268
15
202
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
25.263
15
5
X-RAY DIFFRACTION
r_chiral_restr
0.132
0.2
155
X-RAY DIFFRACTION
r_gen_planes_refined
0.008
0.02
809
X-RAY DIFFRACTION
r_nbd_refined
0.243
0.2
412
X-RAY DIFFRACTION
r_nbtor_refined
0.322
0.2
718
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.157
0.2
57
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.222
0.2
62
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.165
0.2
9
X-RAY DIFFRACTION
r_mcbond_it
1.807
1.5
657
X-RAY DIFFRACTION
r_mcangle_it
5.987
20
1031
X-RAY DIFFRACTION
r_scbond_it
11.645
20
476
X-RAY DIFFRACTION
r_scangle_it
5.213
4.5
406
LS精密化 シェル
解像度: 2.04→2.095 Å / Total num. of bins used: 20
Rfactor
反射数
%反射
Rfree
0.532
21
-
Rwork
0.326
291
-
all
-
312
-
obs
-
-
45.55 %
精密化 TLS
手法: refined / Origin x: 0.9503 Å / Origin y: 5.2605 Å / Origin z: 36.9146 Å