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 | 0.15 | 0.2052 | 0.2 | | |
| 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 |
