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Crystal structure of Bovine heart cytochrome c oxidase, the structure complexed with an allosteric inhibitor T113
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5B1A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 6.8 277 sodium phosphate, PEG4000, decyl maltoside, ethylene glycol, DMSO, T113
Crystal Properties Matthews coefficient Solvent content 3.38 63.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 182.097 α = 90 b = 204.337 β = 90 c = 177.933 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 100 CCD RAYONIX MX225HE 2016-11-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B1 1.000 SPring-8 BL26B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 29.98 0.997 0.064 0.074 0.998 14.8 3.83 648256 32.22
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.33 0.989 0.386 0.452 0.921 3.7 3.71
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5b1a 2.2 29.98 0.92 648256 16655 99.73 0.1793 0.178 0.1807 0.2044 0.2068 42.41
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.9545 f_angle_d 0.9322 f_chiral_restr 0.0452 f_bond_d 0.004 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 28355 Nucleic Acid Atoms Solvent Atoms 2495 Heterogen Atoms 2202
Software Software Software Name Purpose REFMAC refinement PHENIX refinement XDS data reduction XDS data scaling MOLREP phasing