3X2Q
X-ray structure of cyanide-bound bovine heart cytochrome c oxidase in the fully oxidized state at 2.0 angstrom resolution
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | batch | 6.8 | 277 | 40mM Sodium phosphate, 0.2% decylmaltoside, PEG 4000, pH 6.8, batch, temperature 277K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
4.12 | 70.17 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 183.678 | α = 90 |
b = 206.675 | β = 90 |
c = 178.201 | 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 | Bruker DIP-6040 | 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) | 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 | 2 | 40 | 99.9 | 0.125 | 18.5 | 7.5 | 451915 | -3 |
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 | 2 | 2.02 | 99.9 | 0.2038 | 1.2 | 6.8 |
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 | 2DYR | 2 | 40 | 428820 | 22863 | 99.91 | 0.18818 | 0.18678 | 0.21437 | RANDOM | 45.026 |
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] | |
1.32 | 1.72 | -3.03 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.891 |
r_dihedral_angle_4_deg | 16.777 |
r_dihedral_angle_3_deg | 16.092 |
r_dihedral_angle_1_deg | 6.43 |
r_scangle_it | 5.175 |
r_scbond_it | 3.502 |
r_angle_refined_deg | 2.332 |
r_mcangle_it | 2.324 |
r_mcbond_it | 1.405 |
r_chiral_restr | 0.173 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 28506 |
Nucleic Acid Atoms | |
Solvent Atoms | 1286 |
Heterogen Atoms | 2172 |
Software
Software | |
---|---|
Software Name | Purpose |
X-PLOR | model building |
REFMAC | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
X-PLOR | phasing |