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CO bound cytochrome c oxidase without pump laser irradiation at 278K
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3AG1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 6.8 277 40 mM sodium phosphate, 0.2 % decyl maltoside, 2% ethylene glycol, PEG 4000
Crystal Properties Matthews coefficient Solvent content 4.24 70.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 184.806 α = 90 b = 208.488 β = 90 c = 177.885 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 277 CCD RAYONIX MX225HE 2015-10-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER SACLA BEAMLINE BL3 1.23970 SACLA BL3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.2 25 97 0.1278 0.9635 15.27 105.91 335213
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.24 97.1 0.2296 0.825 2.98 26.32
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3AG1 2.2 25 317986 17153 96.86 0.174 0.1721 0.1731 0.2089 0.2096 RANDOM 61.111
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] -0.1 3.37 -3.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.807 r_dihedral_angle_4_deg 17.5 r_dihedral_angle_3_deg 17.124 r_dihedral_angle_1_deg 6.72 r_angle_refined_deg 2.042 r_chiral_restr 0.128 r_bond_refined_d 0.018 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 28506 Nucleic Acid Atoms Solvent Atoms 1326 Heterogen Atoms 2264
Software Software Software Name Purpose REFMAC refinement cctbx.xfel data processing cctbx.prime data scaling REFMAC phasing