SFX structure of oxidized cytochrome c oxidase at 2.38 Angstrom resolution
Serial Crystallography (SX)
Starting Model(s)
Initial Refinement Model(s) |
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Type | Source | Accession Code | Details |
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experimental model | PDB | 7TIE | |
Crystallization
Crystalization Experiments |
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ID | Method | pH | Temperature | Details |
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1 | BATCH MODE | 6.8 | 277 | PEG4000, Sodium Phosphate, decylmaltoside |
Crystal Properties |
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Matthews coefficient | Solvent content |
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4.35 | 71.74 |
Crystal Data
Unit Cell |
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Length ( Å ) | Angle ( ˚ ) |
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a = 178.6 | α = 90 |
b = 189.5 | β = 90 |
c = 211.1 | γ = 90 |
Symmetry |
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Space Group | P 21 21 21 |
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Diffraction
Diffraction Experiment |
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol |
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1 | 1 | x-ray | 293 | CCD | RAYONIX MX340-HS | | 2022-04-30 | M | SINGLE WAVELENGTH |
Radiation Source |
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
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1 | FREE ELECTRON LASER | SLAC LCLS BEAMLINE MFX | 1.24 | SLAC LCLS | MFX |
Serial Crystallography
Sample delivery method |
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Diffraction ID | Description | Sample Delivery Method |
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1 | | injection |
Injection |
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Diffraction ID | Description | Flow Rate | Injector Diameter | Injection Power | Injector Nozzle | Filter Size | Carrier Solvent |
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1 | MESH | undefined (µl/min) | undefined (µm) | | | | |
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 |
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1 | 2.38 | 33 | 100 | 0.9746 | 4.6 | 8864.9426 | | 285036 | | | |
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) |
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1 | 2.38 | 2.47 | | | 0.0472 | | | |
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 |
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X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 2.38 | 33 | 285036 | 14182 | 99.922 | 0.234 | 0.2322 | 0.2657 | 32.959 |
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] |
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-0.037 | | | 0.054 | | -0.018 |
RMS Deviations |
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Key | Refinement Restraint Deviation |
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r_dihedral_angle_2_deg | 33.975 |
r_dihedral_angle_3_deg | 18.865 |
r_dihedral_angle_4_deg | 18.432 |
r_lrange_it | 9.742 |
r_lrange_other | 9.691 |
r_dihedral_angle_1_deg | 7.875 |
r_dihedral_angle_other_3_deg | 6.401 |
r_mcangle_it | 5.051 |
r_mcangle_other | 5.051 |
r_scangle_it | 4.825 |
RMS Deviations |
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Key | Refinement Restraint Deviation |
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r_dihedral_angle_2_deg | 33.975 |
r_dihedral_angle_3_deg | 18.865 |
r_dihedral_angle_4_deg | 18.432 |
r_lrange_it | 9.742 |
r_lrange_other | 9.691 |
r_dihedral_angle_1_deg | 7.875 |
r_dihedral_angle_other_3_deg | 6.401 |
r_mcangle_it | 5.051 |
r_mcangle_other | 5.051 |
r_scangle_it | 4.825 |
r_scangle_other | 4.825 |
r_mcbond_it | 3.167 |
r_mcbond_other | 3.167 |
r_scbond_it | 2.958 |
r_scbond_other | 2.958 |
r_angle_refined_deg | 1.742 |
r_angle_other_deg | 1.145 |
r_metal_ion_refined | 0.385 |
r_symmetry_xyhbond_nbd_refined | 0.271 |
r_xyhbond_nbd_refined | 0.236 |
r_nbd_refined | 0.234 |
r_symmetry_nbd_other | 0.201 |
r_nbd_other | 0.2 |
r_symmetry_nbd_refined | 0.181 |
r_nbtor_refined | 0.179 |
r_symmetry_xyhbond_nbd_other | 0.107 |
r_symmetry_nbtor_other | 0.083 |
r_chiral_restr | 0.07 |
r_bond_refined_d | 0.011 |
r_gen_planes_refined | 0.007 |
r_gen_planes_other | 0.002 |
r_bond_other_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement |
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Non-Hydrogen Atoms | Number |
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Protein Atoms | 28496 |
Nucleic Acid Atoms | |
Solvent Atoms | 601 |
Heterogen Atoms | 2368 |
Software
Software |
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Software Name | Purpose |
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REFMAC | refinement |
CrystFEL | data reduction |
CrystFEL | data scaling |
MOLREP | phasing |