2YIU

X-ray structure of the dimeric cytochrome BC1 complex from the soil bacterium paracoccus denitrificans at 2.7 angstrom resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2QJYPDB ENTRY 2QJY

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
14.6100 MM SODIUM ACETATE, PH 4.6, 50 MM NACL, 30% 2-METHYL 2,4-PENTANDIOL (MPD)
Crystal Properties
Matthews coefficientSolvent content
3.5966

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85.3α = 90
b = 164.91β = 103.18
c = 100.61γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDKIRKPATRICK-BAEZ MIRROR PAIR2009-08-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I03DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.754.97950.133.73.17005540.7
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.72.85900.322.23.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2QJY2.797.9666493353594.340.240330.237660.29049RANDOM28.805
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]
0.86-0.220.47-1.43
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.032
r_dihedral_angle_4_deg19.668
r_dihedral_angle_3_deg18.929
r_dihedral_angle_1_deg6.764
r_scangle_it3.021
r_scbond_it1.942
r_angle_refined_deg1.761
r_mcangle_it1.267
r_mcbond_it0.673
r_chiral_restr0.103
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.032
r_dihedral_angle_4_deg19.668
r_dihedral_angle_3_deg18.929
r_dihedral_angle_1_deg6.764
r_scangle_it3.021
r_scbond_it1.942
r_angle_refined_deg1.761
r_mcangle_it1.267
r_mcbond_it0.673
r_chiral_restr0.103
r_bond_refined_d0.015
r_gen_planes_refined0.008
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 AtomsNumber
Protein Atoms12644
Nucleic Acid Atoms
Solvent Atoms6
Heterogen Atoms340

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing