3SWW
Crystal structure of human dpp-iv in complex with sa-(+)-3-(aminomethyl)-4-(2,4-dichlorophenyl)-6-(2-methoxyphenyl)- 2-methyl-5h-pyrrolo[3,4-b]pyridin-7(6h)-one
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3NOX | 3NOX.PDB |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8.5 | 298 | 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). SUFFICIENT 100 MM LIGAND STOCK SOLUTION (NEAT DMSO) ADDED TO ACHIEVE 1 MM LIGAND CONCENTRATION. SOAKED OVERNIGHT. HARVESTED DIRECTLY AND CRYO-STORED IN LN2 VAPOR DIFFUSION / HANGING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.69 | 54.35 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 65.534 | ¦Á = 90 |
b = 67.928 | ¦Â = 90 |
c = 423.472 | ¦Ã = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | ADSC Q315 | 2005-06-08 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X29A | NSLS | X29A |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot | ||||||||
1,1 | 2 | 50 | 84.9 | 0.113 | 22.9 | 6.7 | 110050 | 32.8 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1,1 | 2 | 2.07 | 40.8 | 0.323 | 3.1 | 2.7 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | 3NOX.PDB | 2 | 47.163 | 1.45 | 109947 | 5540 | 84.8 | 0.1985 | 0.1966 | 0.2342 | 36.2037 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
3.9664 | 4.3715 | -8.3379 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 15.579 |
f_angle_d | 1.09 |
f_chiral_restr | 0.079 |
f_bond_d | 0.007 |
f_plane_restr | 0.004 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 11788 |
Nucleic Acid Atoms | |
Solvent Atoms | 431 |
Heterogen Atoms | 246 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
CBASS | data collection |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
AMoRE | phasing |