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Bovine heart cytochrome c oxidase in the carbon monoxide-bound mixed-valence state at 1.68 angstrom resolution (50 K)
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 40mM Sodium phosphate, 0.2% decylmaltoside, 2% EG, PEG 4000
Crystal Properties Matthews coefficient Solvent content 4.06 69.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 181.491 α = 90 b = 203.303 β = 90 c = 177.484 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 50 CCD RAYONIX MX300HE 2013-06-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.68 200 99.9 0.09 0.094 0.028 9.7 10.2 737777
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.68 1.69 100 1.132 1.201 0.397 0.832 8.9
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5B1A 1.68 39.624 1.33 736437 37025 99.84 0.1538 0.1526 0.1531 0.1771 0.1772 RANDOM
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 18.524 f_angle_d 1.722 f_chiral_restr 0.099 f_bond_d 0.015 f_plane_restr 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 28449 Nucleic Acid Atoms Solvent Atoms 2829 Heterogen Atoms 3148
Software Software Software Name Purpose PHENIX refinement SCALEPACK data scaling DENZO data reduction REFMAC phasing PDB_EXTRACT data extraction