6NKN
Time-resolved SFX structure of the PR intermediate of cytochrome c oxidase at room temperature
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2DYR |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | BATCH MODE | 6.8 | 277 | 36 hour crystallization in a cold room with stirring |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.4 | 72.05 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 178.7 | α = 90 |
b = 189.8 | β = 90 |
c = 211.3 | 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 | 293 | PIXEL | CS-PAD XPP | 2016-12-07 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | FREE ELECTRON LASER | SLAC LCLS BEAMLINE MFX | 1.306 | SLAC LCLS | MFX |
Serial Crystallography
Sample delivery method | ||
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Diffraction ID | Description | Sample Delivery Method |
1 | injection |
Injection | |||||||
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Diffraction ID | Description | Flow Rate | Injector Diameter | Injection Power | Injector Nozzle | Filter Size | Carrier Solvent |
1 | GDVN |
Measurement | |||||
---|---|---|---|---|---|
Diffraction ID | Pulse Duration | Pulse Repetition Rate | Focal Spot Size | Pulse Energy | Photons Per Pulse |
1 | 40 | 120 | 9.5 |
Data Reduction | |||
---|---|---|---|
Diffraction ID | Frames Indexed | Crystal Hits | Total Frames |
1 | 98993 | 108241 |
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 | 2.5 | 10.5 | 98.54 | 0.989 | 5.1 | 1038 | 231448 |
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 | 2.5 | 2.561 | 100 | 0.168 | 0.56 |
Refinement
Statistics | |||||||||||||||||||
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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 | 2.5 | 10.5 | 231448 | 12143 | 98.54 | 0.17777 | 0.17565 | 0.21736 | RANDOM | 63.44 |
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] | |
-2.5 | 0.95 | 1.55 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.896 |
r_dihedral_angle_3_deg | 17.771 |
r_dihedral_angle_4_deg | 17.572 |
r_long_range_B_refined | 11.656 |
r_long_range_B_other | 11.656 |
r_scangle_other | 8.667 |
r_mcangle_it | 7.367 |
r_mcangle_other | 7.367 |
r_dihedral_angle_1_deg | 7.099 |
r_scbond_it | 5.517 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 28419 |
Nucleic Acid Atoms | |
Solvent Atoms | 772 |
Heterogen Atoms | 2228 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
CrystFEL | data reduction |
CrystFEL | data scaling |
PHASER | phasing |