Joint X-ray/neutron structure of cationic trypsin in complex with 2-aminopyridine
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 4I8H | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 277 | 0.2 M ammonium sulfate, 0.1 M Hepes pH 7.5, 15.5-16.5% (w/v) PEG 8000 |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.33 | 47.28 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 54.989 | α = 90 |
| b = 58.537 | β = 90 |
| c = 67.618 | 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 | x-ray | 295 | PIXEL | DECTRIS PILATUS 6M | 2015-06-10 | M | SINGLE WAVELENGTH | ||||||
| 2 | 1 | neutron | 295 | IMAGE PLATE | MAATEL BIODIFF | 2015-07-25 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) | 0.7069 | PETRA III, EMBL c/o DESY | P14 (MX2) |
| 2 | NUCLEAR REACTOR | FRM II BEAMLINE BIODIFF | 2.675 | FRM II | BIODIFF |
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 | 0.939 | 42.662 | 99.7 | 0.041 | 28.59 | 8.75 | 141985 | ||||||||||||
| 2 | 1.42 | 25 | 90.7 | 0.094 | 8.493 | 2.6 | 38142 | ||||||||||||
| 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 | 0.939 | 1 | 0.633 | 4.29 | 8.581 | ||||||||||||||
| 2 | 1.42 | 1.45 | 0.414 | 2.051 | 2 | ||||||||||||||
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 | ||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | 0.939 | 16.935 | 1.36 | 141879 | 7170 | 99.74 | 0.0989 | 0.0986 | 0.1044 | Random selection | ||||||||
| NEUTRON DIFFRACTION | MOLECULAR REPLACEMENT | 1.42 | 22.13 | 38107 | 1913 | 90.76 | 0.1705 | 0.1699 | 0.181 | Random selection | |||||||||
| 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 | 13.953 |
| f_dihedral_angle_d | 13.953 |
| f_angle_d | 1.234 |
| f_angle_d | 1.234 |
| f_chiral_restr | 0.098 |
| f_chiral_restr | 0.098 |
| f_plane_restr | 0.008 |
| f_plane_restr | 0.008 |
| f_bond_d | 0.007 |
| f_bond_d | 0.007 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 1608 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 161 |
| Heterogen Atoms | 13 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| PHENIX | refinement |
| XDS | data reduction |
| HKL-2000 | data reduction |
| XDS | data scaling |
| HKL-2000 | data scaling |
| PHASER | phasing |
| Coot | model building |














