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Time-resolve SFX structure of a photoproduct of carbon monoxide complex of bovine cytochrome c oxidase
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DYR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 6.8 277 PEG4000, Sodium Phosphate, decylmaltoside
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 178.3 α = 90 b = 189 β = 90 c = 209 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 PIXEL CS-PAD CXI-1 2016-06-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER SLAC LCLS BEAMLINE CXI 1.321 SLAC LCLS CXI
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 injection
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 1.759 32.45 100 0.859 6.92 6.9 172414
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 2.87 2.99 100 0.226
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 2.8 32.002 172414 8688 99.355 0.225 0.223 0.2265 0.2687 0.2678 58.179
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] -1.65 0.949 0.701
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.052 r_dihedral_angle_3_deg 18.243 r_dihedral_angle_other_3_deg 16.272 r_dihedral_angle_4_deg 15.967 r_lrange_it 9.789 r_lrange_other 9.789 r_dihedral_angle_1_deg 7.345 r_scangle_it 6.493 r_scangle_other 6.493 r_mcangle_it 6.053
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.052 r_dihedral_angle_3_deg 18.243 r_dihedral_angle_other_3_deg 16.272 r_dihedral_angle_4_deg 15.967 r_lrange_it 9.789 r_lrange_other 9.789 r_dihedral_angle_1_deg 7.345 r_scangle_it 6.493 r_scangle_other 6.493 r_mcangle_it 6.053 r_mcangle_other 6.053 r_scbond_it 3.927 r_scbond_other 3.927 r_mcbond_it 3.717 r_mcbond_other 3.716 r_angle_refined_deg 1.553 r_angle_other_deg 1.13 r_nbd_refined 0.217 r_symmetry_nbd_refined 0.215 r_symmetry_nbd_other 0.18 r_nbtor_refined 0.175 r_xyhbond_nbd_refined 0.163 r_nbd_other 0.16 r_symmetry_xyhbond_nbd_refined 0.13 r_symmetry_xyhbond_nbd_other 0.101 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.072 r_metal_ion_refined 0.059 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 28488 Nucleic Acid Atoms Solvent Atoms 245 Heterogen Atoms 2248
Software Software Software Name Purpose REFMAC refinement CrystFEL data reduction CrystFEL data scaling MOLREP phasing