Neutron Structure of Compound I intermediate of Cytochrome c Peroxidase - Deuterium exchanged 100 K
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | 6 | PH 6.0 | ||
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.1 | 60.38 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 51.19 | α = 90 |
| b = 75.83 | β = 90 |
| c = 107.59 | 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 | 100 | CCD | RIGAKU SATURN 944+ | OSMIC HF | 2013-08-01 | M | SINGLE WAVELENGTH | |||||
| 2 | 1 | neutron | 100 | IMAGE PLATE | FRM II | OSMIC HF | 2013-08-01 | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | ROTATING ANODE | RIGAKU MICROMAX-007 HF | 1.5418 | ||
| 2 | NUCLEAR REACTOR | FRM II BEAMLINE BIODIFF | 3.39 | 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 | 2.18 | 50 | 99.3 | 0.074 | 16.5 | 4.7 | 22053 | ||||||||||||
| 2 | 2.3 | 50 | 90.7 | 0.173 | 4.6 | 2.3 | 13661 | ||||||||||||
| 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 | 2.18 | 2.25 | 0.428 | 5.9 | 1.7 | ||||||||||||||
| 2 | 2.5 | 2.59 | 0.428 | 1.5 | 1.7 | ||||||||||||||
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 | 2.182 | 17.057 | 1.38 | 22053 | 1104 | 98.38 | 0.1516 | 0.1488 | 0.1452 | 0.2052 | 0.1982 | |||||||
| NEUTRON DIFFRACTION | MOLECULAR REPLACEMENT | 2.501 | 46.225 | 1.34 | 13661 | 683 | 90.67 | 0.1914 | 0.1873 | 0.272 | |||||||||
| 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] | |
| 0.0213 | 2.2575 | -3.5349 | ||||
| -1.9296 | 6.9359 | -5.0063 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 15.757 |
| f_angle_d | 1.261 |
| f_chiral_restr | 0.091 |
| f_bond_d | 0.011 |
| f_plane_restr | 0.007 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 2356 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 315 |
| Heterogen Atoms | 43 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| PHENIX | phasing |
| PHENIX | refinement |
| DENZO | data reduction |
| SCALEPACK | data scaling |














