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X-ray structure of the dimeric cytochrome BC1 complex from the soil bacterium paracoccus denitrificans at 2.7 angstrom resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QJY PDB ENTRY 2QJY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.6 100 MM SODIUM ACETATE, PH 4.6, 50 MM NACL, 30% 2-METHYL 2,4-PENTANDIOL (MPD)
Crystal Properties Matthews coefficient Solvent content 3.59 66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.3 α = 90 b = 164.91 β = 103.18 c = 100.61 γ = 90
Symmetry Space Group P 1 21 1
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 ADSC CCD KIRKPATRICK-BAEZ MIRROR PAIR 2009-08-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.7 54.97 95 0.13 3.7 3.1 70055 40.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.85 90 0.32 2.2 3.1
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 PDB ENTRY 2QJY 2.7 97.96 66493 3535 94.34 0.24033 0.23766 0.2388 0.29049 0.2903 RANDOM 28.805
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 -0.22 0.47 -1.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.032 r_dihedral_angle_4_deg 19.668 r_dihedral_angle_3_deg 18.929 r_dihedral_angle_1_deg 6.764 r_scangle_it 3.021 r_scbond_it 1.942 r_angle_refined_deg 1.761 r_mcangle_it 1.267 r_mcbond_it 0.673 r_chiral_restr 0.103
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.032 r_dihedral_angle_4_deg 19.668 r_dihedral_angle_3_deg 18.929 r_dihedral_angle_1_deg 6.764 r_scangle_it 3.021 r_scbond_it 1.942 r_angle_refined_deg 1.761 r_mcangle_it 1.267 r_mcbond_it 0.673 r_chiral_restr 0.103 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12644 Nucleic Acid Atoms Solvent Atoms 6 Heterogen Atoms 340
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing