AUTHORS STATE THAT THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAINS THAT FORM A DIMER BASED ON CRYSTAL PACKING ANALYSIS.
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実験情報
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実験
実験
手法: X線回折 / 使用した結晶の数: 1
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試料調製
結晶
マシュー密度: 5.42 Å3/Da / 溶媒含有率: 77.32 %
結晶化
温度: 277 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 7 詳細: 1.1M sodium citrate, 0.15M sodium chloride, 0.1M TRIS pH 7.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K, VAPOR DIFFUSION, SITTING DROP
モノクロメーター: Single crystal Si(111) bent monochromator (horizontal focusing) 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: 2.7→29.136 Å / Num. obs: 8775 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 103.91 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 22.2
反射 シェル
解像度 (Å)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Num. unique obs
Diffraction-ID
% possible all
2.7-2.8
0.991
2.2
13982
1700
1
98.8
2.8-2.91
0.605
3.6
14401
1656
1
100
2.91-3.04
0.351
6.1
14216
1633
1
100
3.04-3.2
0.192
10.5
14719
1690
1
100
3.2-3.4
0.106
17.6
14587
1677
1
100
3.4-3.66
0.075
23.2
14329
1652
1
99.9
3.66-4.03
0.051
33
14500
1683
1
100
4.03-4.6
0.04
39.4
14395
1669
1
99.9
4.6-5.77
0.036
42
14186
1644
1
100
5.77-29.136
0.034
44.1
14583
1722
1
98.7
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位相決定
位相決定
手法: 単波長異常分散
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解析
ソフトウェア
名称
バージョン
分類
NB
REFMAC
5.2.0019
精密化
PHENIX
精密化
SHELX
位相決定
MolProbity
3beta29
モデル構築
XSCALE
データスケーリング
PDB_EXTRACT
3.004
データ抽出
XDS
データ削減
SHELXD
位相決定
autoSHARP
位相決定
精密化
構造決定の手法: 単波長異常分散 / 解像度: 2.7→29.136 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.964 / SU B: 13.998 / SU ML: 0.127 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.228 / ESU R Free: 0.189 立体化学のターゲット値: MAXIMUM LIKELIHOOD WITH PHASES 詳細: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...詳細: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. AN UNKNOWN LIGAND (UNL) HAS BEEN TENTATIVELY MODELED AT WHAT APPEARS TO BE THE PUTATIVE ACTIVE SITE(S) SURROUNDED BY RESIDUES HIS5, PHE39, GLU53, ARG57, HIS73, ASP107, GLU111 AND GLU123.
Rfactor
反射数
%反射
Selection details
Rfree
0.198
416
4.7 %
RANDOM
Rwork
0.172
-
-
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obs
0.173
8766
99.8 %
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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: 1.2 Å / 溶媒モデル: MASK
原子変位パラメータ
Biso mean: 57.474 Å2
精密化ステップ
サイクル: LAST / 解像度: 2.7→29.136 Å
タンパク質
核酸
リガンド
溶媒
全体
原子数
996
0
9
2
1007
拘束条件
Refine-ID
タイプ
Dev ideal
Dev ideal target
数
X-RAY DIFFRACTION
r_bond_refined_d
0.012
0.022
1017
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
666
X-RAY DIFFRACTION
r_angle_refined_deg
1.657
1.935
1378
X-RAY DIFFRACTION
r_angle_other_deg
0.959
3
1618
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
4.031
5
125
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
29.224
24.6
50
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
12.377
15
168
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
19.148
15
5
X-RAY DIFFRACTION
r_chiral_restr
0.095
0.2
150
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.02
1150
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
216
X-RAY DIFFRACTION
r_nbd_refined
0.218
0.2
179
X-RAY DIFFRACTION
r_nbd_other
0.185
0.2
647
X-RAY DIFFRACTION
r_nbtor_refined
0.188
0.2
494
X-RAY DIFFRACTION
r_nbtor_other
0.085
0.2
520
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.376
0.2
32
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.147
0.2
5
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.206
0.2
27
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.216
0.2
3
X-RAY DIFFRACTION
r_mcbond_it
1.373
3
681
X-RAY DIFFRACTION
r_mcbond_other
0.243
3
261
X-RAY DIFFRACTION
r_mcangle_it
2.134
5
995
X-RAY DIFFRACTION
r_scbond_it
3.973
8
449
X-RAY DIFFRACTION
r_scangle_it
5.127
11
383
LS精密化 シェル
解像度: 2.701→2.771 Å / Total num. of bins used: 20
Rfactor
反射数
%反射
Rfree
0.504
35
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Rwork
0.427
607
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all
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642
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obs
-
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100 %
精密化 TLS
手法: refined / Origin x: 59.8985 Å / Origin y: 22.1081 Å / Origin z: 31.8695 Å