Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O
Has protein modification
Y
Sequence details
FIVE ADDITIONAL N-TERMINAL RESIDUES DUE TO PRESCISSION PROTEASE CLEAVAGE SYNTHETIC PEPTIDE (CHAIN B) ...FIVE ADDITIONAL N-TERMINAL RESIDUES DUE TO PRESCISSION PROTEASE CLEAVAGE SYNTHETIC PEPTIDE (CHAIN B) CORRESPONDING TO YOPD56-65 FROM YERSINIA ENTEROCOLITICA VIRULENCE PLASMID PYVE227 FROM STRAIN W22703.N-TERMINALLY ACETYLATED AND C-TERMINALLY AMIDATED
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 4.82 Å3/Da / Density % sol: 74.5 % / Description: NONE
Crystal grow
Temperature: 293 K / Method: vapor diffusion Details: RESERVOIR SOLUTION: 50 MM MES PH 6, 50 MM CITRATE PH 5, 1.1-1.4 M (NH4)2SO4. VAPOR DIFFUSION AT 293 K WITH DROP RATIO OF 1 TO 0.5 PROTEIN TO RESERVOIR. PROTEIN CONCENTRATION 8 MG/ML. 1.3 ...Details: RESERVOIR SOLUTION: 50 MM MES PH 6, 50 MM CITRATE PH 5, 1.1-1.4 M (NH4)2SO4. VAPOR DIFFUSION AT 293 K WITH DROP RATIO OF 1 TO 0.5 PROTEIN TO RESERVOIR. PROTEIN CONCENTRATION 8 MG/ML. 1.3 FOLD MOLAR EXCESS OF PEPTIDE OVER PROTEIN.
Resolution: 2.5→23.676 Å / SU ML: 0.85 / σ(F): 1.34 / Phase error: 21.84 / Stereochemistry target values: ML Details: RESIDUES 21-28 AND 160-163 FROM CHAIN A ARE DISORDERED, RESIDUES 65 FROM CHAIN B IS DISORDERED
Rfactor
Num. reflection
% reflection
Rfree
0.2381
588
4.9 %
Rwork
0.1899
-
-
obs
0.1921
11901
99.32 %
Solvent computation
Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.501 Å2 / ksol: 0.301 e/Å3
Displacement parameters
Biso mean: 79.2 Å2
Baniso -1
Baniso -2
Baniso -3
1-
5.2738 Å2
0 Å2
0 Å2
2-
-
5.2738 Å2
0 Å2
3-
-
-
-10.5477 Å2
Refinement step
Cycle: LAST / Resolution: 2.5→23.676 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1116
0
35
17
1168
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.007
1180
X-RAY DIFFRACTION
f_angle_d
1.061
1585
X-RAY DIFFRACTION
f_dihedral_angle_d
16.576
441
X-RAY DIFFRACTION
f_chiral_restr
0.069
176
X-RAY DIFFRACTION
f_plane_restr
0.006
201
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
2.5002-2.7515
0.3482
164
0.3134
2751
X-RAY DIFFRACTION
98
2.7515-3.1489
0.2732
133
0.2176
2805
X-RAY DIFFRACTION
100
3.1489-3.9642
0.2034
145
0.1721
2845
X-RAY DIFFRACTION
100
3.9642-23.6769
0.2344
146
0.1797
2912
X-RAY DIFFRACTION
99
Refinement TLS params.
Method: refined / Refine-ID: X-RAY DIFFRACTION
ID
L11 (°2)
L12 (°2)
L13 (°2)
L22 (°2)
L23 (°2)
L33 (°2)
S11 (Å °)
S12 (Å °)
S13 (Å °)
S21 (Å °)
S22 (Å °)
S23 (Å °)
S31 (Å °)
S32 (Å °)
S33 (Å °)
T11 (Å2)
T12 (Å2)
T13 (Å2)
T22 (Å2)
T23 (Å2)
T33 (Å2)
Origin x (Å)
Origin y (Å)
Origin z (Å)
1
1.2046
-1.5407
-0.4412
2.7405
1.3438
0.9526
0.5375
0.0997
-0.553
-0.5779
-0.3269
-0.595
-0.3099
0.2135
-0.0929
0.4624
-0.1076
0.1249
0.5539
0.1867
0.8502
-37.5842
6.5256
13.9266
2
0.4564
0.009
-0.384
2.1747
-0.3361
0.3516
0.3206
-0.4733
-0.0915
0.5288
-0.3763
-0.2229
0.0043
-0.0865
0
0.6
-0.033
-0.0939
0.4523
0.1098
0.6452
-44.6207
9.1016
19.3299
3
0.5936
0.1137
-0.7129
2.2745
1.1947
1.596
0.2166
-0.7345
-0.1423
0.3567
-0.3481
0.4026
-0.2058
-0.4551
0.0004
0.6152
-0.1332
-0.0001
0.5231
0.0154
0.4375
-51.9521
21.0169
23.2856
4
0.7776
0.0562
0.5202
0.8949
0.5699
0.6202
-0.2382
0.8343
0.5467
-0.8087
-0.0595
-0.1046
-1.4513
-0.127
-0.1002
1.0553
0.023
0.0969
0.8329
-0.1076
0.5453
-52.1704
32.9422
17.8576
5
1.7825
-0.06
0.107
0.604
0.8952
1.3102
0.2165
0.3571
2.3842
-1.1572
-0.6712
-0.7293
-1.1272
0.0846
0.0001
0.7198
-0.0197
-0.0944
0.5053
-0.0103
0.8931
-41.0187
18.5051
11.7015
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
CHAINAAND (RESSEQ29:56)
2
X-RAY DIFFRACTION
2
CHAINAAND (RESSEQ57:86)
3
X-RAY DIFFRACTION
3
CHAINAAND (RESSEQ87:133)
4
X-RAY DIFFRACTION
4
CHAINAAND (RESSEQ134:159)
5
X-RAY DIFFRACTION
5
CHAINB
+
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