Type VI secretion system, lipoprotein SciN / Type VI secretion system, lipoprotein SciN / Type VI secretion protein SciN-like superfamily / Type VI secretion lipoprotein, VasD, EvfM, TssJ, VC_A0113 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin-like / Sandwich / Mainly Beta / Type VI secretion system lipoprotein TssJ
温度: 293 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 6 詳細: mixing 300 nL protein at 8mg/mL with 100 nL 2.2 M AmSO4, 0.2 M Na+-thiocyanate pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
解像度: 1.35→1.39 Å / Rmerge(I) obs: 0.311 / Mean I/σ(I) obs: 2.8 / % possible all: 79.5
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解析
ソフトウェア
名称
バージョン
分類
ADSC
Quantum
データ収集
MOLREP
位相決定
REFMAC
5.6.0116
精密化
XDS
データ削減
XSCALE
データスケーリング
精密化
構造決定の手法: 分子置換 開始モデル: CsI SAD crystal structure 解像度: 1.35→40 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.972 / SU B: 1.275 / SU ML: 0.024 / 交差検証法: THROUGHOUT / ESU R: 0.048 / ESU R Free: 0.045 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD / 詳細: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
Rfactor
反射数
%反射
Selection details
Rfree
0.15982
1773
5 %
RANDOM
Rwork
0.13683
-
-
-
obs
0.13798
33535
96.63 %
-
all
-
33535
-
-
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: 19.15 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.42 Å2
0.21 Å2
-0 Å2
2-
-
0.42 Å2
-0 Å2
3-
-
-
-0.62 Å2
Refine analyze
Luzzati coordinate error free: 0.045 Å
精密化ステップ
サイクル: LAST / 解像度: 1.35→40 Å
タンパク質
核酸
リガンド
溶媒
全体
原子数
1000
0
5
200
1205
拘束条件
Refine-ID
タイプ
Dev ideal
Dev ideal target
数
X-RAY DIFFRACTION
r_bond_refined_d
0.01
0.02
1204
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.527
1.986
1675
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.723
5
173
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
36.506
24.182
55
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
12.107
15
217
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
10.059
15
11
X-RAY DIFFRACTION
r_chiral_restr
0.093
0.2
195
X-RAY DIFFRACTION
r_gen_planes_refined
0.008
0.021
955
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
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
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
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
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
X-RAY DIFFRACTION
r_scbond_it
X-RAY DIFFRACTION
r_scangle_it
X-RAY DIFFRACTION
r_rigid_bond_restr
2.4
3
1204
X-RAY DIFFRACTION
r_sphericity_free
24.427
5
45
X-RAY DIFFRACTION
r_sphericity_bonded
13.568
5
1319
LS精密化 シェル
解像度: 1.35→1.385 Å / Total num. of bins used: 20
Rfactor
反射数
%反射
Rfree
0.237
94
-
Rwork
0.202
1938
-
obs
-
-
78.82 %
精密化 TLS
手法: refined / Origin x: -17.3791 Å / Origin y: 36.3314 Å / Origin z: -4.3242 Å