Structure of porcine pancreatic elastase complexed with a potent peptidyl inhibitor FR130180 determined by neutron crystallography
NEUTRON DIFFRACTION - X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) |
|---|
| Type | Source | Accession Code | Details |
|---|
|
experimental model | PDB | 3HGP | PDB ENTRY 3HGPPDB ENTRY 3HGP |
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | VAPOR DIFFUSION, SITTING DROP | 5 | 293 | 0.3M sodium sulphate, 0.05M D-substituted sodium acetate, pH5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 2.12 | 42.03 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 50.937 | α = 90 |
| b = 57.464 | β = 90 |
| c = 75.18 | γ = 90 |
| Symmetry |
|---|
| Space Group | P 21 21 21 |
|---|
Diffraction
| Diffraction Experiment |
|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol |
|---|
| 1 | 1 | neutron | 293 | IMAGE PLATE | NEUTRON IMAGING PLATE | | 2006-09-19 | M | SINGLE WAVELENGTH |
| 2 | 1 | x-ray | 293 | CCD | ADSC QUANTUM 4r | | 2008-05-28 | M | SINGLE WAVELENGTH |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | NUCLEAR REACTOR | | 2.9 | | |
| 2 | SYNCHROTRON | PHOTON FACTORY BEAMLINE BL-6A | 1.0 | Photon Factory | BL-6A |
Data Collection
| Overall |
|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | R Split (All) | 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 | 1.65 | 42.17 | 88.9 | 0.098 | | | | | | 11.3 | 3 | | 24296 | | -3 | 10.06 |
| Highest Resolution Shell |
|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | R Merge I (Observed) | R-Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | R Split (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) |
|---|
| 1 | 1.65 | 1.71 | | 0.328 | | | | | | 3.9 | 2.6 | 2065 |
Refinement
| Statistics |
|---|
| Diffraction ID | Structure Solution Method | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | Cut-off Sigma (F) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B |
|---|
| NEUTRON DIFFRACTION | | 1.65 | 42.169 | | | | 23486 | 1127 | 86.3 | | 0.1973 | 0.1964 | | 0.2161 | | RANDOM | 15.3 |
| X-RAY DIFFRACTION | | 1.201 | 45.655 | | | | 66319 | 3374 | 95.45 | | 0.1494 | 0.1487 | 0.36 | 0.1625 | 0.37 | RANDOM | |
| 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] |
|---|
| | | | | |
| | | | | |
| RMS Deviations |
|---|
| Key | Refinement Restraint Deviation |
|---|
| f_dihedral_angle_d | 22.449 |
| f_angle_d | 3.066 |
| f_chiral_restr | 0.171 |
| f_bond_d | 0.026 |
| f_plane_restr | 0.022 |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 1822 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 190 |
| Heterogen Atoms | 42 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| PHENIX | refinement |
| DENZO | data reduction |
| SCALEPACK | data scaling |
