DATA FROM A CRYSTAL OF SE-MET SUBSTITUTED PROTEIN WAS USED FOR THE MAD PHASING EXPERIMENTS AND DATA FROM A CRYSTAL OF NATIVE PROTEIN WAS USED FOR THE FINAL REFINEMENT.
2
結晶化
温度 (K)
Crystal-ID
手法
pH
詳細
277
1
蒸気拡散法, シッティングドロップ法, nanodrop
7.3
0.2M KFormate, 20.0% PEG-3350, No Buffer pH 7.3, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K
解像度: 1.74→99 Å / Num. obs: 61062 / % possible obs: 98.69 % / 冗長度: 4.73 % / Biso Wilson estimate: 32.84 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 30.27
反射 シェル
解像度: 1.74→1.77 Å / 冗長度: 3.37 % / Rmerge(I) obs: 0.428 / Mean I/σ(I) obs: 3.61 / Num. unique all: 2652 / % possible all: 86.87
-
解析
ソフトウェア
名称
バージョン
分類
MOSFLM
データ削減
SCALEPACK
データスケーリング
SOLVE
位相決定
REFMAC
5.2.0005
精密化
精密化
構造決定の手法: 多波長異常分散 / 解像度: 1.75→43.78 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.635 / SU ML: 0.062 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.094 立体化学のターゲット値: MAXIMUM LIKELIHOOD WITH PHASES 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS ELECTRON DENSITY FOR RESIDUES ALA42 AND LYS43 ARE POOR, SO THESE TWO RESIDUES ARE NOT INCLUDED IN THE FINAL MODEL. THE DATA USED IN THE FINAL ...詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS ELECTRON DENSITY FOR RESIDUES ALA42 AND LYS43 ARE POOR, SO THESE TWO RESIDUES ARE NOT INCLUDED IN THE FINAL MODEL. THE DATA USED IN THE FINAL REFINEMENT WAS FROM A NATIVE CRYSTAL. THE REFINEMENT OF THE COORDINATES WAS RESTRAINED WITH THE EXPERIMENTAL PHASES FROM A SELENOMETHIONINE MAD EXPERIMENT FROM A SECOND CRYSTAL.
Rfactor
反射数
%反射
Selection details
Rfree
0.20393
3091
5.1 %
RANDOM
Rwork
0.17822
-
-
-
obs
0.17951
57756
99.22 %
-
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: 34.34 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.26 Å2
0 Å2
0 Å2
2-
-
0.8 Å2
0 Å2
3-
-
-
-1.06 Å2
精密化ステップ
サイクル: LAST / 解像度: 1.75→43.78 Å
タンパク質
核酸
リガンド
溶媒
全体
原子数
3329
0
8
378
3715
拘束条件
Refine-ID
タイプ
Dev ideal
Dev ideal target
数
X-RAY DIFFRACTION
r_bond_refined_d
0.017
0.022
3555
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
3199
X-RAY DIFFRACTION
r_angle_refined_deg
1.644
1.959
4820
X-RAY DIFFRACTION
r_angle_other_deg
0.832
3
7468
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.56
5
471
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
36.044
24.768
151
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
11.442
15
630
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
21.042
15
20
X-RAY DIFFRACTION
r_chiral_restr
0.102
0.2
530
X-RAY DIFFRACTION
r_gen_planes_refined
0.007
0.02
4089
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
713
X-RAY DIFFRACTION
r_nbd_refined
0.206
0.2
684
X-RAY DIFFRACTION
r_nbd_other
0.178
0.2
3303
X-RAY DIFFRACTION
r_nbtor_other
0.088
0.2
2226
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.139
0.2
266
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.104
0.2
14
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.255
0.2
50
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.107
0.2
24
X-RAY DIFFRACTION
r_mcbond_it
2.324
3
2336
X-RAY DIFFRACTION
r_mcbond_other
0.593
3
942
X-RAY DIFFRACTION
r_mcangle_it
3.22
5
3636
X-RAY DIFFRACTION
r_scbond_it
5.427
8
1420
X-RAY DIFFRACTION
r_scangle_it
7.32
11
1184
X-RAY DIFFRACTION
r_nbtor_refined
0.179
0.2
1791
LS精密化 シェル
解像度: 1.75→1.795 Å / Total num. of bins used: 20
Rfactor
反射数
%反射
Rfree
0.272
252
5.71 %
Rwork
0.218
4159
-
obs
-
-
98.59 %
精密化 TLS
手法: refined / Origin x: 12.6584 Å / Origin y: 20.6205 Å / Origin z: 35.9151 Å