Neutron Structure of Ferric Cytochrome c Peroxidase - Deuterium exchanged at room temperature
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | | 6 | | PH 6.0 |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 3.18 | 61.27 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 51.7 | α = 90 |
| b = 76.8 | β = 90 |
| c = 107.6 | 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 | 290 | IMAGE PLATE | MAR scanner 345 mm plate | | 2013-10-01 | M | |
| 2 | 1 | neutron | 290 | IMAGE PLATE | | | 2013-08-01 | | |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | SEALED TUBE | Xenocs GeniX 3D Cu HF | 1.5418 | | |
| 2 | NUCLEAR REACTOR | ILL BEAMLINE LADI III | 3.2-4.2 | ILL | LADI III |
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 | 2.1 | 14.8 | 94.7 | 0.061 | | | | | | 14.6 | 3.5 | | 24307 | | | |
| 2 | 2.4 | 39.7 | 73.8 | 0.151 | | | | | | 7.6 | 3.8 | | 12695 | | | |
| 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 | 2.1 | 2.15 | | 0.243 | | | | | | 4.6 | 2.4 | |
| 2 | 2.4 | 2.53 | | 0.194 | | | | | | 4.4 | 2.4 | |
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 | | 2.1 | 14.77 | | 1.37 | | 24307 | 2430 | 94.9 | | 0.1381 | 0.1337 | 0.1294 | 0.1766 | 0.1679 | | |
| NEUTRON DIFFRACTION | | 2.407 | 39.84 | | 1.58 | | 12695 | 1270 | 73.76 | | 0.1826 | 0.1759 | | 0.2433 | | | |
| 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] |
|---|
| 2.1778 | | | 5.9821 | | -8.1599 |
| -2.5352 | | | 9.999 | | -7.4638 |
| RMS Deviations |
|---|
| Key | Refinement Restraint Deviation |
|---|
| f_dihedral_angle_d | 17.659 |
| f_dihedral_angle_d | 17.659 |
| f_angle_d | 1.349 |
| f_angle_d | 1.349 |
| f_chiral_restr | 0.089 |
| f_chiral_restr | 0.089 |
| f_bond_d | 0.012 |
| f_bond_d | 0.012 |
| f_plane_restr | 0.008 |
| f_plane_restr | 0.008 |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 2357 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 198 |
| Heterogen Atoms | 43 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| PHENIX | model building |
| PHENIX | refinement |
| LAUEGEN | data reduction |
| SCALA | data scaling |
| PHENIX | phasing |
| PHENIX | phasing |
| PHENIX | phasing |
