- PDB-3q0t: Crystal structure of human dpp-iv in complex withsa-(+)- methyl2-... -
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Open data
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Basic information
Entry
Database: PDB / ID: 3q0t
Title
Crystal structure of human dpp-iv in complex withsa-(+)- methyl2-(3-(aminomethyl)-4-(2,4-dichlorophenyl)-2-methyl- 7-oxo-5h-pyrrolo[3,4-b]pyridin-6(7h)-yl)acetate
Mass: 18.015 Da / Num. of mol.: 431 / Source method: isolated from a natural source / Formula: H2O
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.67 Å3/Da / Density % sol: 53.94 %
Crystal grow
Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: CRYSTALS GROWN IN 2 UL EQUIVOLUME MIXTURE OF PROTEIN SOLUTION (0.1 M NACL, 20 MM TRIS-HCL BUFFER PH 7.8, 9.8 MG/ML PROTEIN) AND CRYSTALLIZATION SOLUTION (17% W/V PEG 3350, 15% W/V GLYCEROL, ...Details: CRYSTALS GROWN IN 2 UL EQUIVOLUME MIXTURE OF PROTEIN SOLUTION (0.1 M NACL, 20 MM TRIS-HCL BUFFER PH 7.8, 9.8 MG/ML PROTEIN) AND CRYSTALLIZATION SOLUTION (17% W/V PEG 3350, 15% W/V GLYCEROL, 200 MM MGCL2, 100 MM TRIS-HCL BUFFER PH 8.5). SUFFICIENT. 100 MM LIGAND STOCK SOLUTION (NEAT DMSO) ADDED TO ACHIEVE 1 MM LIGAND CONCENTRATION. SOAKED OVERNIGHT. HARVESTED DIRECTLY AND CRYO-STORED IN LN2. 2. temperature 298K, VAPOR DIFFUSION, HANGING DROP
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Data collection
Diffraction source
Source: SYNCHROTRON / Site: NSLS / Beamline: X29A
Radiation
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Relative weight: 1
Reflection
Resolution: 2.4→50 Å / Num. obs: 71882 / % possible obs: 96.1 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.068 / Χ2: 0.938 / Net I/σ(I): 10.6
Reflection shell
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Num. unique all
Χ2
Diffraction-ID
% possible all
2.4-2.49
5.4
0.441
5576
0.853
1
75.9
2.49-2.59
5.8
0.412
6617
0.86
1
89.9
2.59-2.7
7
0.355
7181
0.886
1
97.2
2.7-2.85
7.7
0.277
7350
0.887
1
99.4
2.85-3.02
7.9
0.18
7331
0.925
1
99.6
3.02-3.26
8
0.114
7406
0.959
1
99.7
3.26-3.58
7.9
0.071
7425
0.992
1
99.8
3.58-4.1
7.8
0.049
7527
0.985
1
99.8
4.1-5.17
7.8
0.04
7560
1.05
1
99.9
5.17-50
7.4
0.029
7909
0.9
1
99.4
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Processing
Software
Name
Version
Classification
NB
DENZO
datareduction
SCALEPACK
datascaling
PHENIX
dev_606
refinement
PDB_EXTRACT
3.1
dataextraction
Refinement
Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3NOX
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