5XDQ
Bovine heart cytochrome c oxidase in the fully oxidized state with pH 7.3 at 1.77 angstrom resolution
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1V54 |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | BATCH MODE | 7.3 | 277 | 3% polythylene glycol (PEG), 0.35% decal maltose, 0.70% fluorinated octyl-maltoside, 33mM sodium acetate, 25mM Tris-HCL (pH 7.3) |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 183.307 | α = 90 |
b = 205.904 | β = 90 |
c = 177.526 | γ = 90 |
Symmetry | |
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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 MX-225 | 2014-07-09 | 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 | |||||||||||||||||||
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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 | 1.77 | 200 | 99.9 | 0.086 | 13 | 8.9 | 643861 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1 | 1.77 | 1.79 | 100 | 8.2 | 16039 |
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 | 1V54 | 1.77 | 134.453 | 611017 | 32361 | 99.59 | 0.1652 | 0.1639 | 0.1904 | RANDOM | 45.057 |
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] | |
-0.29 | 6.37 | -6.08 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.805 |
r_sphericity_free | 25.121 |
r_sphericity_bonded | 23.645 |
r_dihedral_angle_3_deg | 13.76 |
r_dihedral_angle_4_deg | 13.607 |
r_dihedral_angle_1_deg | 5.164 |
r_rigid_bond_restr | 2.409 |
r_angle_refined_deg | 1.203 |
r_chiral_restr | 0.082 |
r_gen_planes_refined | 0.02 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 28442 |
Nucleic Acid Atoms | |
Solvent Atoms | 2883 |
Heterogen Atoms | 2542 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
SCALEPACK | data scaling |
PDB_EXTRACT | data extraction |
DENZO | data reduction |
MOLREP | phasing |