6JY3
Monomeric Form of Bovine Heart Cytochrome c Oxidase in the Fully Oxidized State
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 5B1A | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | BATCH MODE | 277 | sodium phosphate, PEG 4000, DM | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 4.84 | 74.6 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( ? ) | Angle ( ? ) |
| a = 149.529 | ¦Á = 90 |
| b = 152.131 | ¦Â = 90 |
| c = 174.083 | ¦Ã = 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 | 50 | CCD | RAYONIX MX225HE | 2011-07-27 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | SPRING-8 BEAMLINE BL44XU | 0.9 | SPring-8 | BL44XU |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | Rpim I (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 | 1.8 | 200 | 99.3 | 0.031 | 29.3 | 7.4 | 361138 | ||||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
| 1 | 1.8 | 1.82 | 0.459 | 0.765 | 2 | ||||||||||||||
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 | 5B1A | 1.85 | 40 | 316483 | 16494 | 99.04 | 0.15326 | 0.15125 | 0.19162 | RANDOM | 43.877 | ||||||
| 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] | |
| 0.86 | 3.49 | -4.35 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_sphericity_free | 48.503 |
| r_dihedral_angle_2_deg | 34.292 |
| r_sphericity_bonded | 25.134 |
| r_dihedral_angle_4_deg | 15.806 |
| r_dihedral_angle_3_deg | 14.15 |
| r_scangle_other | 10.151 |
| r_scbond_it | 9.66 |
| r_scbond_other | 9.66 |
| r_long_range_B_refined | 9.148 |
| r_long_range_B_other | 9.09 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 13851 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 662 |
| Heterogen Atoms | 729 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| DENZO | data reduction |
| SCALEPACK | data scaling |
| MOLREP | phasing |
