7QZR
Structure of native leukocyte myeloperoxidase in complex with the Staphyloccal Peroxidase Inhibitor SPIN from Staphylococcus aureus
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5UZU |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 9 | 298 | 8% (w/V) PEG 20000, 0.1 M BICINE pH 9, 0.5% (V/V) Dioxane |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.53 | 51.43 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 112.085 | α = 90 |
b = 112.085 | β = 90 |
c = 249.949 | 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 | 213.15 | PIXEL | DECTRIS PILATUS3 X 2M | 2020-11-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID23-2 | 0.873 | ESRF | ID23-2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | 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 | 2.18 | 19.814 | 92.9 | 0.28 | 0.2998 | 0.1049 | 0.988 | 6.19 | 7.63 | 68945 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
2.18 | 2.327 | 48.4 | 1.2199 | 1.355 | 0.582 | 0.512 | 1.57 | 5.28 | 3448 |
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 | 5UZU | 2.18 | 19.81 | 68945 | 3513 | 82.4 | 0.2059 | 0.2038 | 0.2438 | RANDOM | 32.35 |
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] | |
0.0188 | 0.0188 | -0.0376 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
t_other_torsion | 14.98 |
t_omega_torsion | 3.26 |
t_angle_deg | 0.98 |
t_bond_d | 0.008 |
t_dihedral_angle_d | |
t_gen_planes | |
t_it | |
t_nbd | |
t_chiral_improper_torsion | |
t_ideal_dist_contact |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 10274 |
Nucleic Acid Atoms | |
Solvent Atoms | 526 |
Heterogen Atoms | 372 |
Software
Software | |
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Software Name | Purpose |
autoPROC | data processing |
Aimless | data scaling |
STARANISO | data scaling |
BUSTER | refinement |
autoPROC | data reduction |
PHASER | phasing |