metabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to bacterium / metal ion binding 類似検索 - 分子機能
Lysozyme - #10 / Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Lysozyme / Lysozyme-like domain superfamily ...Lysozyme - #10 / Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha 類似検索 - ドメイン・相同性
モノクロメーター: silicon si111 / 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: 1 Å / 相対比: 1
反射
解像度: 1.94→65.938 Å / Num. obs: 15888 / % possible obs: 99.7 % / Biso Wilson estimate: 20.804 Å2
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解析
ソフトウェア
名称
バージョン
分類
REFMAC
5.1.24
精密化
MOSFLM
データ削減
CCP4
(SCALA)
データスケーリング
XFIT
データ削減
精密化
構造決定の手法: 分子置換 / 解像度: 1.941→19.57 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.891 / SU B: 4.187 / SU ML: 0.124 / 交差検証法: THROUGHOUT / ESU R: 0.205 / ESU R Free: 0.186 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD / 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
反射数
%反射
Selection details
Rfree
0.25001
792
5 %
RANDOM
Rwork
0.18049
-
-
-
obs
0.1839
15044
99.81 %
-
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: 1.4 Å / 溶媒モデル: BABINET MODEL WITH MASK
原子変位パラメータ
Biso mean: 24.614 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.01 Å2
0 Å2
0 Å2
2-
-
0.01 Å2
0 Å2
3-
-
-
-0.01 Å2
精密化ステップ
サイクル: LAST / 解像度: 1.941→19.57 Å
タンパク質
核酸
リガンド
溶媒
全体
原子数
2020
0
20
98
2138
拘束条件
Refine-ID
タイプ
Dev ideal
Dev ideal target
数
X-RAY DIFFRACTION
r_bond_refined_d
0.031
0.021
2090
X-RAY DIFFRACTION
r_bond_other_d
0.002
0.02
1722
X-RAY DIFFRACTION
r_angle_refined_deg
2.234
1.924
2814
X-RAY DIFFRACTION
r_angle_other_deg
1.102
3
4050
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
8.12
5
256
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
X-RAY DIFFRACTION
r_chiral_restr
0.139
0.2
280
X-RAY DIFFRACTION
r_gen_planes_refined
0.012
0.02
2332
X-RAY DIFFRACTION
r_gen_planes_other
0.007
0.02
432
X-RAY DIFFRACTION
r_nbd_refined
0.241
0.2
480
X-RAY DIFFRACTION
r_nbd_other
0.262
0.2
1966
X-RAY DIFFRACTION
r_nbtor_refined
X-RAY DIFFRACTION
r_nbtor_other
0.093
0.2
1093
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.208
0.2
95
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
1.291
0.2
69
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.28
0.2
83
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.229
0.2
13
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
1.478
1.5
1276
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
2.439
2
2018
X-RAY DIFFRACTION
r_scbond_it
3.596
3
814
X-RAY DIFFRACTION
r_scangle_it
5.082
4.5
796
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: 1.941→1.991 Å / Total num. of bins used: 20 /