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: 2.46→50 Å / Num. obs: 7821 / % possible obs: 97.6 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.043 / Χ2: 1.131 / Net I/σ(I): 19.9
Reflection shell
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Num. unique all
Χ2
% possible all
2.46-2.55
5.3
0.131
781
0.297
99.2
2.55-2.65
5.5
0.103
797
0.346
99.5
2.65-2.77
5.5
0.094
807
0.456
99.8
2.77-2.92
5.5
0.073
803
0.619
99.9
2.92-3.1
5.6
0.064
792
0.922
99.9
3.1-3.34
5.6
0.055
818
1.242
99.9
3.34-3.67
5
0.051
613
1.517
78.9
3.67-4.21
5.5
0.048
802
2.21
99.5
4.21-5.3
5.7
0.037
808
1.936
100
5.3-50
5.7
0.035
800
1.777
99
-
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: 2.46→22.667 Å / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.779 / SU ML: 0.32 / σ(F): 1.97 / 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
0.246
354
4.54 %
Rwork
0.21
-
-
obs
0.211
7790
97.25 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.975 Å2 / ksol: 0.362 e/Å3
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