ProteinaseK / Endopeptidase K / Tritirachium alkaline proteinase
Mass: 28958.791 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Engyodontium album (fungus) / Gene: PROK / Production host: Engyodontium album (fungus) / References: UniProt: P06873, peptidase K
Mass: 18.015 Da / Num. of mol.: 68 / Source method: isolated from a natural source / Formula: H2O
Sequence details
Residue 207 is unambiguously identified as ASP from the electron density map even though the ...Residue 207 is unambiguously identified as ASP from the electron density map even though the corresponding UNP DATABASE contains SER.
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION
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Sample preparation
Crystal
Density Matthews: 2.24 Å3/Da / Density % sol: 45.13 %
Crystal grow
Temperature: 291 K / Method: batch mode / Details: NaNO3, CaCl2, MES
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Data collection
Diffraction
Mean temperature: 300 K
Diffraction source
Source: FREE ELECTRON LASER / Site: SACLA / Beamline: BL3 / Wavelength: 1.77 Å
Detector
Type: MPCCD / Detector: CCD / Date: Nov 25, 2014
Radiation
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1.77 Å / Relative weight: 1
Reflection
Resolution: 2.3→30 Å / Num. obs: 12263 / % possible obs: 100 % / Redundancy: 402 % / Net I/σ(I): 12.4
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Processing
Software
Name
Version
Classification
PHENIX
1.8.4_1496
refinement
CrystFEL
datascaling
Refinement
Resolution: 2.3→29.659 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.09 / Stereochemistry target values: ML
Rfactor
Num. reflection
% reflection
Rfree
0.1812
611
4.98 %
Rwork
0.141
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obs
0.1429
12263
99.99 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement step
Cycle: LAST / Resolution: 2.3→29.659 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2031
0
1
68
2100
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.008
2072
X-RAY DIFFRACTION
f_angle_d
1.055
2813
X-RAY DIFFRACTION
f_dihedral_angle_d
12.781
717
X-RAY DIFFRACTION
f_chiral_restr
0.043
312
X-RAY DIFFRACTION
f_plane_restr
0.004
371
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
2.3-2.5314
0.2236
144
0.1616
2825
X-RAY DIFFRACTION
100
2.5314-2.8974
0.2379
140
0.1799
2879
X-RAY DIFFRACTION
100
2.8974-3.6493
0.2056
165
0.1544
2887
X-RAY DIFFRACTION
100
3.6493-29.6615
0.1397
162
0.1173
3061
X-RAY DIFFRACTION
100
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