4X1N
The crystal structure of mupain-1-16 in complex with murinised human uPA at pH7.4
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2NWN |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 4.6 | 298 | 2.0M ammonium sulfate, 50mM sodium citrate pH 4.6, 5% PEG 400 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.05 | 39.92 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 121.595 | ¦Á = 90 |
b = 121.595 | ¦Â = 90 |
c = 42.4 | ¦Ã = 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 315 | 2011-05-06 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRF BEAMLINE BL17U | 0.979 | SSRF | BL17U |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 50 | 98.7 | 21312 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 2NWN | 1.8 | 35.13 | 20223 | 1089 | 98.46 | 0.23214 | 0.22971 | 0.27619 | RANDOM | 39.92 |
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] | |
-0.92 | -0.92 | -0.92 | 2.98 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.093 |
r_dihedral_angle_4_deg | 22.061 |
r_dihedral_angle_3_deg | 16.17 |
r_dihedral_angle_1_deg | 6.268 |
r_angle_refined_deg | 1.23 |
r_angle_other_deg | 0.733 |
r_chiral_restr | 0.068 |
r_bond_refined_d | 0.007 |
r_gen_planes_refined | 0.005 |
r_bond_other_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2028 |
Nucleic Acid Atoms | |
Solvent Atoms | 65 |
Heterogen Atoms | 9 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
Coot | model building |