2YEV
Structure of caa3-type cytochrome oxidase
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2OCC | PDB ENTRY 2OCC |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | LIPIDIC CUBIC PHASE | 5 | 16-21% PEG 400, 0.1 M NA CITRATE PH 4.5-5.0, 0-0.1 M LITHIUM SULPHATE, 0.1 M NACL. CRYSTALLISED USING THE LIPIDIC CUBIC PHASE USING 7.7 MAG AS THE HOSTING LIPID. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.78 | 55.83 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 127.25 | α = 90 |
b = 76.03 | β = 92.21 |
c = 300.267 | γ = 90 |
Symmetry | |
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Space Group | I 1 2 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | MARRESEARCH | TWO K-B PAIRS OF BIMORPH TYPE MIRRORS | 2010-06-17 | M | SINGLE WAVELENGTH | |||||
2 | 1 | x-ray | 100 | CCD | MARRESEARCH | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 23-ID-B | APS | 23-ID-B | |
2 | SYNCHROTRON | DIAMOND BEAMLINE I24 | Diamond | I24 |
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 | 2.36 | 53.48 | 100 | 0.16 | 9.5 | 8.4 | 118251 | -3 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 2.36 | 2.49 | 100 | 0.98 | 2.3 | 8.2 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | PDB ENTRY 2OCC | 2.36 | 77.179 | 1.37 | 118243 | 5969 | 99.95 | 0.1736 | 0.1712 | 0.2183 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
-1.392 | -3.4644 | 6.891 | -5.499 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 14.532 |
f_angle_d | 1.084 |
f_chiral_restr | 0.063 |
f_bond_d | 0.006 |
f_plane_restr | 0.004 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 18560 |
Nucleic Acid Atoms | |
Solvent Atoms | 392 |
Heterogen Atoms | 630 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
XDS | data reduction |
XSCALE | data scaling |
PHASER | phasing |