Serial synchrotron crystallography structure of ba3-type cytochrome c oxidase from Thermus thermophilus using a goniometer compatible flow-cell
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 | 5NDC | |
Crystallization
Crystalization Experiments |
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ID | Method | pH | Temperature | Details |
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1 | LIPIDIC CUBIC PHASE | 5.3 | 298 | 1.4 M NaCl, 100 mM MES pH 5.3 with 36 % to 39 % (v/v) PEG 400 |
Crystal Properties |
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Matthews coefficient | Solvent content |
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3.3 | 62.69 |
Crystal Data
Unit Cell |
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Length ( Å ) | Angle ( ˚ ) |
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a = 146.06 | α = 90 |
b = 100.17 | β = 126.76 |
c = 96.62 | γ = 90 |
Symmetry |
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Space Group | C 1 2 1 |
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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 | 298 | PIXEL | DECTRIS EIGER X 16M | | 2019-12-13 | M | SINGLE WAVELENGTH |
Radiation Source |
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
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1 | SYNCHROTRON | MAX IV BEAMLINE BioMAX | 0.98 | MAX IV | BioMAX |
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 | Capillary-based flow-cell | 1.2 (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 | 2.12 | 25.802 | 100 | 0.99 | 6.8 | 123.6 | | 65010 | | | |
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 | 2.12 | 2.2 | | | 0.52 | | | |
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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | Mean Isotropic B |
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X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 2.12 | 25.802 | 63185 | 3207 | 99.932 | 0.154 | 0.152 | 0.16 | 0.1844 | 0.19 | 48.819 |
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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0.014 | | 0.007 | -0.016 | | -0.004 |
RMS Deviations |
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Key | Refinement Restraint Deviation |
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r_dihedral_angle_2_deg | 32.985 |
r_dihedral_angle_4_deg | 21.384 |
r_dihedral_angle_3_deg | 14.473 |
r_lrange_it | 8.128 |
r_lrange_other | 8.128 |
r_scangle_it | 6.886 |
r_scangle_other | 6.885 |
r_dihedral_angle_1_deg | 6.262 |
r_mcangle_it | 4.861 |
r_mcangle_other | 4.861 |
RMS Deviations |
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Key | Refinement Restraint Deviation |
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r_dihedral_angle_2_deg | 32.985 |
r_dihedral_angle_4_deg | 21.384 |
r_dihedral_angle_3_deg | 14.473 |
r_lrange_it | 8.128 |
r_lrange_other | 8.128 |
r_scangle_it | 6.886 |
r_scangle_other | 6.885 |
r_dihedral_angle_1_deg | 6.262 |
r_mcangle_it | 4.861 |
r_mcangle_other | 4.861 |
r_scbond_it | 4.689 |
r_scbond_other | 4.688 |
r_mcbond_it | 3.664 |
r_mcbond_other | 3.662 |
r_angle_refined_deg | 1.72 |
r_angle_other_deg | 1.276 |
r_symmetry_nbd_refined | 0.272 |
r_symmetry_xyhbond_nbd_refined | 0.222 |
r_nbd_refined | 0.221 |
r_nbd_other | 0.188 |
r_symmetry_nbd_other | 0.178 |
r_nbtor_refined | 0.174 |
r_xyhbond_nbd_refined | 0.13 |
r_metal_ion_refined | 0.12 |
r_chiral_restr | 0.083 |
r_symmetry_nbtor_other | 0.079 |
r_bond_refined_d | 0.009 |
r_gen_planes_refined | 0.009 |
r_gen_planes_other | 0.006 |
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 | 5910 |
Nucleic Acid Atoms | |
Solvent Atoms | 104 |
Heterogen Atoms | 384 |
Software
Software |
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Software Name | Purpose |
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REFMAC | refinement |
CrystFEL | data reduction |
CrystFEL | data scaling |
PHASER | phasing |