Structure of native leukocyte myeloperoxidase in complex with a truncated version of the Staphylococcal Peroxidase Inhibitor SPIN and iodide at pH 5.5
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 7Z53 | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 5.5 | 295.15 | 0.1 M Na Acet 5.5 pH 6 %(w/v) PEG 8K 10 %(w/v) PEG 1K 0.4 M NaI |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.33 | 47.19 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 111.361 | α = 90 |
| b = 111.361 | β = 90 |
| c = 242.068 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 43 21 2 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 213.15 | PIXEL | DECTRIS EIGER X 16M | Toroidal mirror | 2023-03-05 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ESRF BEAMLINE ID23-1 | 1.9075 | ESRF | ID23-1 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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 | 2.63 | 101.17 | 93.8 | 0.343 | 0.359 | 0.105 | 0.931 | 6.9 | 11.5 | 38848 | |||||||||
| 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) | ||||||||
| 1 | 2.63 | 2.81 | 55.7 | 2.538 | 2.657 | 0.782 | 0.578 | 1.4 | |||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | |||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 2.63 | 101.17 | 36923 | 1925 | 84.68 | 0.19498 | 0.19217 | 0.199 | 0.2494 | 0.2546 | RANDOM | 48.555 | |||||
| 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] | |
| -0.58 | -0.58 | 1.17 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_3_deg | 15.689 |
| r_dihedral_angle_2_deg | 12.802 |
| r_long_range_B_refined | 6.738 |
| r_long_range_B_other | 6.732 |
| r_dihedral_angle_1_deg | 6.588 |
| r_scangle_other | 4.363 |
| r_mcangle_it | 3.364 |
| r_mcangle_other | 3.363 |
| r_scbond_it | 2.705 |
| r_scbond_other | 2.705 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 10077 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 273 |
| Heterogen Atoms | 434 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| Aimless | data scaling |
| XDS | data reduction |
| MOLREP | phasing |
