4YM9
Crystal structure of Porcine Pancreatic Elastase (PPE) in complex with the novel inhibitor JM102
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2V35 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.1 | 295.15 | 200 mM Na2SO4 100 mM NaCH3COO |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.15 | 42.8 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 51.026 | α = 90 |
b = 58.34 | β = 90 |
c = 74.923 | γ = 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 | Bruker Platinum 135 | 2010-05-10 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | BRUKER AXS MICROSTAR | 1.54 |
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 | 1.8 | 46.03 | 94 | 0.046 | 30.4 | 10.4 | 19425 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.8 | 1.9 | 67.9 | 0.1475 | 5.2 | 1.33 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation 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 | FREE R-VALUE | 2V35 | 1.8 | 38.408 | 0.03 | 37784 | 1859 | 94.14 | 0.1302 | 0.1288 | 0.1567 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 14.705 |
f_angle_d | 1.305 |
f_chiral_restr | 0.051 |
f_bond_d | 0.011 |
f_plane_restr | 0.006 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1822 |
Nucleic Acid Atoms | |
Solvent Atoms | 158 |
Heterogen Atoms | 69 |
Software
Software | |
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Software Name | Purpose |
SAINT | data reduction |
SADABS | data scaling |
PHASER | phasing |
PHENIX | refinement |