5C9M
The structure of oxidized rat cytochrome c (T28A) at 1.362 angstroms resolution.
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 295 | 20 mg/ml protein, PEG 4000, isopropanol, sodium acetate, potassium ferricyanate |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.27 | 45.7 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 34.517 | α = 109.86 |
| b = 52.567 | β = 92.93 |
| c = 61.771 | γ = 92.2 |
| Symmetry | |
|---|---|
| Space Group | P 1 |
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 | MARMOSAIC 225 mm CCD | 2014-11-18 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | APS BEAMLINE 21-ID-F | 0.97872 | APS | 21-ID-F |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 1.362 | 57.962 | 92.37 | 0.052 | 14.1 | 3.9 | 80448 | 76544 | 13 | ||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
| 1 | 1.362 | 1.398 | 66.24 | 0.58 | 2.2 | 3.8 | |||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 5C0Z | 1.362 | 57.96 | 76544 | 3901 | 92.37 | 0.131 | 0.129 | 0.16982 | RANDOM | 21.413 | ||||||
| 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] | |
| 0.04 | 0.04 | 0.89 | -0.51 | 0.85 | -0.22 | |
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_sphericity_free | 35.915 |
| r_dihedral_angle_2_deg | 31.917 |
| r_dihedral_angle_4_deg | 31.575 |
| r_sphericity_bonded | 12.158 |
| r_dihedral_angle_3_deg | 12.075 |
| r_dihedral_angle_1_deg | 6.497 |
| r_long_range_B_refined | 3.725 |
| r_long_range_B_other | 3.046 |
| r_rigid_bond_restr | 2.519 |
| r_scangle_other | 2.45 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 3220 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 472 |
| Heterogen Atoms | 224 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| PHENIX | phasing |
| Aimless | data scaling |
| XDS | data reduction |
