6WXZ
CRYSTAL STRUCTURE OF MYELOPEROXIDASE SUBFORM C (MPO) COMPLEX WITH Compound-29 A.K.A 7-(1,2-DIPHENYLETHYL)-1H-[1,2,3]TRIAZOLO[4,5-B]PYRIDIN-5-AMINE
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5QJ2 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 296 | 0.1M Hepes pH 7.5, 150mM NaCl, 20-25%(V/V)PEG3350.Crystals were cryoprotected by supplementing the mother liquor with 15% (v/v) ethylene glycol and harvested by flash-cooling in liquid nitrogen |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.65 | 53.55 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 107.416 | α = 90 |
b = 107.416 | β = 90 |
c = 239.631 | γ = 90 |
Symmetry | |
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Space Group | P 43 21 2 |
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 | PIXEL | DECTRIS PILATUS 6M | 2011-03-02 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 17-ID | 1.0 | APS | 17-ID |
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 | 2.226 | 239.63 | 100 | 0.069 | 23.7 | 12.8 | 69646 | 48.36 |
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 | 2.226 | 2.35 | 100 | 0.53 | 4.6 | 13.7 |
Refinement
Statistics | |||||||||||||||||||
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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 | 5QJ2 | 2.226 | 98.02 | 69535 | 3514 | 100 | 0.2123 | 0.2107 | 0.2419 | RANDOM | 58.81 |
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] | |
-7.0383 | -7.0383 | 14.0767 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
t_other_torsion | 15.87 |
t_omega_torsion | 3.32 |
t_angle_deg | 0.93 |
t_bond_d | 0.008 |
t_dihedral_angle_d | |
t_trig_c_planes | |
t_gen_planes | |
t_it | |
t_nbd | |
t_improper_torsion |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 9038 |
Nucleic Acid Atoms | |
Solvent Atoms | 432 |
Heterogen Atoms | 366 |
Software
Software | |
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Software Name | Purpose |
BUSTER | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |
SCALA | data scaling |
PHASER | phasing |