peptidase Do / cellular response to misfolded protein / protein quality control for misfolded or incompletely synthesized proteins / serine-type peptidase activity / peptidase activity / outer membrane-bounded periplasmic space / serine-type endopeptidase activity / proteolysis / identical protein binding / plasma membrane Similarity search - Function
Monochromator: Varimax-HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1.5416 Å / Relative weight: 1
Reflection
Resolution: 2.734→50 Å / Num. obs: 55922 / % possible obs: 94.9 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 8.8
Reflection shell
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
% possible all
2.734-2.85
5.3
0.502
95.9
2.85-2.96
5.3
0.372
95.4
2.96-3.1
5.3
0.268
94.6
3.1-3.26
5.4
0.213
94.2
3.26-3.46
5.5
0.166
93.2
3.46-3.73
5.5
0.132
92.1
3.73-4.11
5.5
0.111
91
4.11-4.7
5.4
0.082
93.6
4.7-5.92
6
0.071
99.6
5.92-50
6.3
0.048
99.3
-
Phasing
Phasing
Method: molecular replacement
-
Processing
Software
Name
Version
Classification
NB
DENZO
datareduction
SCALEPACK
datascaling
PHASER
phasing
PHENIX
1.5_2
refinement
PDB_EXTRACT
3.005
dataextraction
StructureStudio
datacollection
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.734→33.819 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.4 / σ(F): 1.34 / Phase error: 28.69 / Stereochemistry target values: ML Details: To obtain the best possible geometry, this structure was refined with hydrogens whose coordinates were determined by the attached heavy atom. Authors state that although hydrogens cannot be ...Details: To obtain the best possible geometry, this structure was refined with hydrogens whose coordinates were determined by the attached heavy atom. Authors state that although hydrogens cannot be visualized at this resolution, they are present and contribute to scattering. The hydrogens are kept in this entry because independent assessment of many aspects of the geometry, including steric clashes, require their presence. Moreover, removing hydrogen atoms after refinement makes independent assessment of refinement statistics effectively irreproducible.
Rfactor
Num. reflection
% reflection
Rfree
0.2699
2852
5.11 %
Rwork
0.2194
-
-
obs
0.222
55770
94.11 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 13.855 Å2 / ksol: 0.321 e/Å3
Displacement parameters
Biso mean: 56.528 Å2
Baniso -1
Baniso -2
Baniso -3
1-
1.626 Å2
-0 Å2
0 Å2
2-
-
-1.757 Å2
-0 Å2
3-
-
-
0.131 Å2
Refinement step
Cycle: LAST / Resolution: 2.734→33.819 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
13375
0
0
208
13583
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.004
13536
X-RAY DIFFRACTION
f_angle_d
0.793
18407
X-RAY DIFFRACTION
f_dihedral_angle_d
14.092
4871
X-RAY DIFFRACTION
f_chiral_restr
0.044
2246
X-RAY DIFFRACTION
f_plane_restr
0.004
2428
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
2.734-2.7814
0.3468
110
0.2632
2227
X-RAY DIFFRACTION
80
2.7814-2.8319
0.3074
136
0.2582
2659
X-RAY DIFFRACTION
96
2.8319-2.8864
0.326
142
0.2485
2639
X-RAY DIFFRACTION
95
2.8864-2.9452
0.344
146
0.2405
2644
X-RAY DIFFRACTION
96
2.9452-3.0092
0.2849
162
0.2344
2621
X-RAY DIFFRACTION
95
3.0092-3.0792
0.3235
134
0.218
2634
X-RAY DIFFRACTION
95
3.0792-3.1562
0.2812
140
0.2193
2641
X-RAY DIFFRACTION
94
3.1562-3.2414
0.3251
149
0.2267
2616
X-RAY DIFFRACTION
94
3.2414-3.3367
0.3142
144
0.2247
2579
X-RAY DIFFRACTION
93
3.3367-3.4443
0.2683
138
0.2167
2606
X-RAY DIFFRACTION
93
3.4443-3.5673
0.2579
156
0.2123
2573
X-RAY DIFFRACTION
93
3.5673-3.71
0.2729
140
0.212
2548
X-RAY DIFFRACTION
91
3.71-3.8786
0.2835
114
0.2176
2567
X-RAY DIFFRACTION
91
3.8786-4.0827
0.2419
130
0.2048
2545
X-RAY DIFFRACTION
90
4.0827-4.338
0.2245
139
0.1766
2588
X-RAY DIFFRACTION
92
4.338-4.6722
0.2087
154
0.1588
2671
X-RAY DIFFRACTION
95
4.6722-5.1409
0.1962
139
0.1735
2847
X-RAY DIFFRACTION
99
5.1409-5.8814
0.2595
155
0.1959
2841
X-RAY DIFFRACTION
100
5.8814-7.3972
0.2672
167
0.2325
2875
X-RAY DIFFRACTION
100
7.3972-33.822
0.2687
157
0.2459
2997
X-RAY DIFFRACTION
99
+
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