3QN7
Potent and selective bicyclic peptide inhibitor (UK18) of human urokinase-type plasminogen activator(uPA)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2NWN | 2NWN.pdb |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 4.3 | 293 | 2M ammonium sulfate, 0.05M sodium citrate, 5%(v/v) PEG 400, pH 4.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2 | 38.46 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 121.25 | α = 90 |
b = 121.25 | β = 90 |
c = 42.72 | γ = 120 |
Symmetry | |
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Space Group | H 3 |
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 QUANTUM 315r | Toroidal focusing mirrors | 2010-10-29 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID14-4 | 0.939 | ESRF | ID14-4 |
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 | 1.9 | 39.57 | 99.8 | 0.079 | 12.2 | 5.4 | 18155 | 18155 |
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 | 1.9 | 2 | 100 | 0.405 | 3.9 | 5.4 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 2NWN.pdb | 1.9 | 39.57 | 18155 | 17487 | 946 | 99.76 | 0.19822 | 0.19822 | 0.19527 | 0.25233 | RANDOM | 34.287 |
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] | |
-0.96 | -0.48 | -0.96 | 1.44 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 27.911 |
r_dihedral_angle_4_deg | 19.594 |
r_dihedral_angle_3_deg | 16.772 |
r_dihedral_angle_1_deg | 7.462 |
r_scangle_it | 4.94 |
r_scbond_it | 3.22 |
r_mcangle_it | 2.344 |
r_angle_refined_deg | 1.9 |
r_mcbond_it | 1.329 |
r_chiral_restr | 0.154 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2050 |
Nucleic Acid Atoms | |
Solvent Atoms | 132 |
Heterogen Atoms | 9 |
Software
Software | |
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Software Name | Purpose |
ADSC | data collection |
PHASES | phasing |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |