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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) Type Source Accession Code Details experimental model PDB 5NDC
Crystallization Crystalization Experiments ID Method pH Temperature Details 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 Matthews coefficient Solvent content 3.3 62.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 146.06 α = 90 b = 100.17 β = 126.76 c = 96.62 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 298 PIXEL DECTRIS EIGER X 16M 2019-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.98 MAX IV BioMAX
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 injection
Injection Diffraction ID Description Flow Rate Injector Diameter Injection Power Injector Nozzle Filter Size Carrier Solvent 1 Capillary-based flow-cell 1.2 (µl/min) undefined (µm)
Data Collection Overall 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 2.12 25.802 100 0.99 6.8 123.6 65010
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.12 2.2 0.52
Refinement Statistics 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 X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.12 25.802 63185 3207 99.932 0.154 0.152 0.1606 0.1844 0.1865 48.819
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] 0.014 0.007 -0.016 -0.004
RMS Deviations Key Refinement Restraint Deviation 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 Key Refinement Restraint Deviation 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 Non-Hydrogen Atoms Number Protein Atoms 5910 Nucleic Acid Atoms Solvent Atoms 104 Heterogen Atoms 384
Software Software Software Name Purpose REFMAC refinement CrystFEL data reduction CrystFEL data scaling PHASER phasing