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Serial femtosecond crystallography structure of photo dissociated CO from ba3- type cytochrome c oxidase determined by extrapolation method
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 5.3 293 34-38 % PEG 400 (v/v), 1.4 M NaCl, pH 5.3
Crystal Properties Matthews coefficient Solvent content 3.3 62.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 145.85 α = 90 b = 100.32 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 293 CCD MPCCD 2018-02-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER SACLA BEAMLINE BL3 0.987 SACLA BL3
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 43.4 94.78 0.91 4 99.1 71307
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 2.071 0.55
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 37.151 71307 1877 94.783 0.397 0.3961 0.4047 0.4354 0.4363 36.97
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] -0.109 0.515 -0.684 0.011
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.42 r_dihedral_angle_6_deg 15.681 r_dihedral_angle_1_deg 7.699 r_dihedral_angle_2_deg 6.649 r_angle_refined_deg 1.84 r_nbtor_refined 0.318 r_nbd_refined 0.244 r_xyhbond_nbd_refined 0.241 r_symmetry_xyhbond_nbd_refined 0.223 r_symmetry_nbd_refined 0.191
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.42 r_dihedral_angle_6_deg 15.681 r_dihedral_angle_1_deg 7.699 r_dihedral_angle_2_deg 6.649 r_angle_refined_deg 1.84 r_nbtor_refined 0.318 r_nbd_refined 0.244 r_xyhbond_nbd_refined 0.241 r_symmetry_xyhbond_nbd_refined 0.223 r_symmetry_nbd_refined 0.191 r_chiral_restr 0.13 r_metal_ion_refined 0.101 r_bond_refined_d 0.01 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5910 Nucleic Acid Atoms Solvent Atoms 178 Heterogen Atoms 386
Software Software Software Name Purpose REFMAC refinement CrystFEL data reduction CrystFEL data scaling PHASER phasing