5A09
Crystal Structure of human neutrophil elastase in complex with a dihydropyrimidone inhibitor
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 1PPG | PDB ENTRY 1PPG |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | 28%PEG4000, 0.1MTRIS/HCL AT PH 8.2, 0.7MLICL | |||
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.28 | 46.1 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 72.77 | α = 90 |
| b = 72.77 | β = 90 |
| c = 69.626 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | P 63 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 100 | CCD | MARRESEARCH | M | SINGLE WAVELENGTH | |||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | MPG/DESY, HAMBURG BEAMLINE BW6 | MPG/DESY, HAMBURG | BW6 | |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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 | 1.81 | 63.25 | 96.4 | 0.1 | 3.9 | 1.1 | |||||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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 | 1.81 | 1.9 | 90.6 | 0.59 | 1.1 | ||||||||||||||
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 | PDB ENTRY 1PPG | 1.81 | 63.25 | 17436 | 947 | 96.5 | 0.18524 | 0.18235 | 0.23944 | RANDOM | 25.866 | ||||||
| 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] | |
| 0.41 | 0.2 | 0.41 | -0.61 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_1_deg | 6.692 |
| r_scangle_it | 3.372 |
| r_scbond_it | 2.076 |
| r_angle_refined_deg | 1.482 |
| r_mcangle_it | 1.426 |
| r_mcbond_it | 0.793 |
| r_symmetry_hbond_refined | 0.339 |
| r_nbd_refined | 0.211 |
| r_xyhbond_nbd_refined | 0.146 |
| r_symmetry_vdw_refined | 0.145 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 1636 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 179 |
| Heterogen Atoms | 95 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| MOSFLM | data reduction |
| SCALA | data scaling |
