PeptidoglycanD,D-transpeptidaseFtsI / Essential cell division protein FtsI / Murein transpeptidase / Penicillin-binding protein 3 / PBP-3 ...Essential cell division protein FtsI / Murein transpeptidase / Penicillin-binding protein 3 / PBP-3 / Peptidoglycan synthase FtsI
Mass: 37129.418 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ftsI, pbpB, b0084, JW0082 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P0AD68, serine-type D-Ala-D-Ala carboxypeptidase
#2: Protein/peptide
Bicyclicpeptideinhibitor
Mass: 1496.774 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Bicyclic peptide with a scaffold covalently linking three cysteine residues. C-terminus is capped with an amine. Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-29N / 1,1',1''-(1,3,5-triazinane-1,3,5-triyl)tripropan-1-one / 1,1',1''-(1,3,5-triazinane-1,3,5-triyl)triprop-2-en-1-one, bound form
Mass: 255.313 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H21N3O3 / Feature type: SUBJECT OF INVESTIGATION
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1 Å / Relative weight: 1
Reflection
Resolution: 1.52→45.04 Å / Num. obs: 50525 / % possible obs: 99.6 % / Redundancy: 12.2 % / CC1/2: 1 / Χ2: 1.01 / Net I/av σ(I): 23.8 / Net I/σ(I): 23.8
Reflection shell
Resolution: 1.52→1.55 Å / Redundancy: 7.1 % / Num. unique obs: 2315 / CC1/2: 0.749 / % possible all: 93
-
Processing
Software
Name
Version
Classification
REFMAC
5.8.0267
refinement
XDS
datareduction
XDS
datascaling
Aimless
0.7.4
datascaling
PHASER
phasing
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.52→45.04 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.015 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.078 / ESU R Free: 0.081 Details: Hydrogens have been added in their riding positions
Rfactor
Num. reflection
% reflection
Rfree
0.2157
2525
4.999 %
Rwork
0.1819
47985
-
all
0.184
-
-
obs
-
50510
99.58 %
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parameters
Biso mean: 24.42 Å2
Baniso -1
Baniso -2
Baniso -3
1-
3.04 Å2
-0 Å2
0 Å2
2-
-
-1.971 Å2
-0 Å2
3-
-
-
-1.069 Å2
Refinement step
Cycle: LAST / Resolution: 1.52→45.04 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2525
0
18
263
2806
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.011
0.013
2636
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.017
2589
X-RAY DIFFRACTION
r_angle_refined_deg
1.738
1.651
3584
X-RAY DIFFRACTION
r_angle_other_deg
1.438
1.574
5949
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.815
5
345
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
30.319
20.403
124
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
13.146
15
429
X-RAY DIFFRACTION
r_dihedral_angle_other_3_deg
17.939
15
3
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
14.285
15
21
X-RAY DIFFRACTION
r_chiral_restr
0.09
0.2
345
X-RAY DIFFRACTION
r_gen_planes_refined
0.01
0.02
2996
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
594
X-RAY DIFFRACTION
r_nbd_refined
0.228
0.2
521
X-RAY DIFFRACTION
r_symmetry_nbd_other
0.187
0.2
2444
X-RAY DIFFRACTION
r_nbtor_refined
0.17
0.2
1292
X-RAY DIFFRACTION
r_symmetry_nbtor_other
0.084
0.2
1228
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.188
0.2
205
X-RAY DIFFRACTION
r_symmetry_xyhbond_nbd_other
0.075
0.2
1
X-RAY DIFFRACTION
r_symmetry_nbd_refined
0.348
0.2
14
X-RAY DIFFRACTION
r_nbd_other
0.262
0.2
67
X-RAY DIFFRACTION
r_symmetry_xyhbond_nbd_refined
0.164
0.2
20
X-RAY DIFFRACTION
r_mcbond_it
2.174
2.301
1353
X-RAY DIFFRACTION
r_mcbond_other
2.169
2.3
1352
X-RAY DIFFRACTION
r_mcangle_it
3.241
3.439
1689
X-RAY DIFFRACTION
r_mcangle_other
3.241
3.44
1690
X-RAY DIFFRACTION
r_scbond_it
2.848
2.7
1283
X-RAY DIFFRACTION
r_scbond_other
2.847
2.7
1284
X-RAY DIFFRACTION
r_scangle_it
4.376
3.906
1889
X-RAY DIFFRACTION
r_scangle_other
4.375
3.907
1890
X-RAY DIFFRACTION
r_lrange_it
6.377
28.839
2971
X-RAY DIFFRACTION
r_lrange_other
6.376
28.842
2972
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
1.52-1.56
0.333
176
0.319
3345
X-RAY DIFFRACTION
94.5489
1.56-1.602
0.277
180
0.269
3416
X-RAY DIFFRACTION
100
1.602-1.649
0.315
176
0.266
3340
X-RAY DIFFRACTION
100
1.649-1.699
0.257
171
0.246
3245
X-RAY DIFFRACTION
100
1.699-1.755
0.273
165
0.218
3137
X-RAY DIFFRACTION
100
1.755-1.817
0.237
161
0.198
3055
X-RAY DIFFRACTION
99.9689
1.817-1.885
0.22
154
0.19
2932
X-RAY DIFFRACTION
100
1.885-1.962
0.208
149
0.184
2847
X-RAY DIFFRACTION
100
1.962-2.049
0.233
144
0.188
2727
X-RAY DIFFRACTION
100
2.049-2.149
0.207
136
0.187
2594
X-RAY DIFFRACTION
100
2.149-2.265
0.207
131
0.174
2484
X-RAY DIFFRACTION
100
2.265-2.403
0.218
124
0.159
2359
X-RAY DIFFRACTION
100
2.403-2.569
0.217
118
0.156
2243
X-RAY DIFFRACTION
100
2.569-2.774
0.198
108
0.16
2045
X-RAY DIFFRACTION
100
2.774-3.039
0.275
101
0.172
1923
X-RAY DIFFRACTION
100
3.039-3.397
0.201
92
0.176
1742
X-RAY DIFFRACTION
100
3.397-3.921
0.173
81
0.165
1554
X-RAY DIFFRACTION
100
3.921-4.799
0.165
71
0.148
1334
X-RAY DIFFRACTION
99.9289
4.799-6.776
0.195
54
0.173
1035
X-RAY DIFFRACTION
100
+
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