5X1B
CO bound cytochrome c oxidase at 20 nsec after pump laser irradiation to release CO from O2 reduction center
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | BATCH MODE | 6.8 | 277 | 40 mM sodium phosphate, 0.2% decyl maltoside, 2% ethylene glycol, PEG 4000 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.26 | 71.13 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 185.849 | α = 90 |
b = 209.485 | β = 90 |
c = 179.524 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | 277 | CCD | RAYONIX MX225HE | 2015-06-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | FREE ELECTRON LASER | SACLA BEAMLINE BL3 | 1.24020 | SACLA | BL3 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | 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 | 2.4 | 14.99 | 98.2 | 0.1624 | 0.9576 | 6.28 | 63.23 | 266141 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.4 | 2.44 | 79.6 | 0.4131 | 0.4967 | 4.61 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | THROUGHOUT | 2.4 | 15 | 252489 | 13569 | 97.67 | 0.1843 | 0.1819 | 0.2296 | RANDOM | 72.697 |
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] | |
-0.89 | 4.94 | -4.05 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.898 |
r_dihedral_angle_3_deg | 18.114 |
r_dihedral_angle_4_deg | 17.423 |
r_dihedral_angle_1_deg | 6.641 |
r_angle_refined_deg | 1.832 |
r_chiral_restr | 0.114 |
r_bond_refined_d | 0.013 |
r_gen_planes_refined | 0.009 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 28506 |
Nucleic Acid Atoms | |
Solvent Atoms | 972 |
Heterogen Atoms | 2236 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
cctbx.xfel | data processing |
cctbx.prime | data scaling |
REFMAC | phasing |