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Monomeric Form of Bovine Heart Cytochrome c Oxidase in the Fully Oxidized State
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 277 sodium phosphate, PEG 4000, DM
Crystal Properties Matthews coefficient Solvent content 4.84 74.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 149.529 α = 90 b = 152.131 β = 90 c = 174.083 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 MX225HE 2011-07-27 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) 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 1.8 200 99.3 0.031 29.3 7.4 361138
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.82 0.459 0.765 2
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 5B1A 1.85 40 316483 16494 99.04 0.15326 0.15125 0.166 0.19162 0.2029 RANDOM 43.877
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] 0.86 3.49 -4.35
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 48.503 r_dihedral_angle_2_deg 34.292 r_sphericity_bonded 25.134 r_dihedral_angle_4_deg 15.806 r_dihedral_angle_3_deg 14.15 r_scangle_other 10.151 r_scbond_it 9.66 r_scbond_other 9.66 r_long_range_B_refined 9.148 r_long_range_B_other 9.09
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 48.503 r_dihedral_angle_2_deg 34.292 r_sphericity_bonded 25.134 r_dihedral_angle_4_deg 15.806 r_dihedral_angle_3_deg 14.15 r_scangle_other 10.151 r_scbond_it 9.66 r_scbond_other 9.66 r_long_range_B_refined 9.148 r_long_range_B_other 9.09 r_mcangle_it 7.233 r_mcangle_other 7.233 r_rigid_bond_restr 6.906 r_mcbond_it 6.665 r_mcbond_other 6.655 r_dihedral_angle_1_deg 5.877 r_angle_refined_deg 2.039 r_angle_other_deg 1.002 r_chiral_restr 0.119 r_bond_refined_d 0.022 r_gen_planes_refined 0.011 r_gen_planes_other 0.005 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13851 Nucleic Acid Atoms Solvent Atoms 662 Heterogen Atoms 729
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing