8K6Y
Serial femtosecond crystallography structure of photo dissociated CO from ba3- type cytochrome c oxidase determined by extrapolation method
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5NDC |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | LIPIDIC CUBIC PHASE | 5.3 | 293 | 34-38 % PEG 400 (v/v), 1.4 M NaCl, pH 5.3 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.3 | 62.69 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 145.85 | α = 90 |
b = 100.32 | β = 126.76 |
c = 96.62 | γ = 90 |
Symmetry | |
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Space Group | C 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 | 293 | CCD | MPCCD | 2018-02-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | FREE ELECTRON LASER | SACLA BEAMLINE BL3 | 0.987 | SACLA | BL3 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 43.4 | 94.78 | 0.91 | 4 | 99.1 | 71307 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2 | 2.071 | 0.55 |
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 (All) | R-Work | R-Free | Mean Isotropic B | ||||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 2 | 37.151 | 71307 | 1877 | 94.783 | 0.397 | 0.3961 | 0.4354 | 36.97 |
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] | |
-0.109 | 0.515 | -0.684 | 0.011 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_3_deg | 17.42 |
r_dihedral_angle_6_deg | 15.681 |
r_dihedral_angle_1_deg | 7.699 |
r_dihedral_angle_2_deg | 6.649 |
r_angle_refined_deg | 1.84 |
r_nbtor_refined | 0.318 |
r_nbd_refined | 0.244 |
r_xyhbond_nbd_refined | 0.241 |
r_symmetry_xyhbond_nbd_refined | 0.223 |
r_symmetry_nbd_refined | 0.191 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5910 |
Nucleic Acid Atoms | |
Solvent Atoms | 178 |
Heterogen Atoms | 386 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
CrystFEL | data reduction |
CrystFEL | data scaling |
PHASER | phasing |