☰ Navigation Tabs
SFX structure of oxidized cytochrome c oxidase at 2.38 Angstrom resolution
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7TIE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 6.8 277 PEG4000, Sodium Phosphate, decylmaltoside
Crystal Properties Matthews coefficient Solvent content 4.35 71.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 178.6 α = 90 b = 189.5 β = 90 c = 211.1 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293 CCD RAYONIX MX340-HS 2022-04-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER SLAC LCLS BEAMLINE MFX 1.24 SLAC LCLS MFX
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 MESH undefined (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 2.38 33 100 0.9746 4.6 8864.9426 285036
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 2.38 2.47 0.0472
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 THROUGHOUT 2.38 33 285036 14182 99.922 0.234 0.2322 0.2341 0.2657 0.2664 32.959
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] -0.037 0.054 -0.018
RMS Deviations Key Refinement Restraint Deviation 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 Key Refinement Restraint Deviation 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 Non-Hydrogen Atoms Number Protein Atoms 28496 Nucleic Acid Atoms Solvent Atoms 601 Heterogen Atoms 2368
Software Software Software Name Purpose REFMAC refinement CrystFEL data reduction CrystFEL data scaling MOLREP phasing