3H1K

Chicken cytochrome BC1 complex with ZN++ and an iodinated derivative of kresoxim-methyl bound


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1BCC1BCC after further correction/refinement

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.727720MM KMES PH 6.7, 75MM NACL, 10% GLYCEROL, AND 6% PEG4000. The Kresoxim-methyl derivative WAS ADDED to the protein FROM ETHANOLIC SOLUTION. After verifying good diffraction by these crystals, some were transferred to a drop of mother liquor supplemented with glycerol and ~0.2 mM ZnCl2. After 1 week this crystal was flash-cooled for data collection. During analysis of Zn binding presence of the inhibitor was overlooked, and in the primary citation publication the anomalous signal of I in the inhibitor was mistakenly attributed to a second Zn binding site, Zn02. VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
4.0669.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 171.717α = 90
b = 181.297β = 90
c = 241.288γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 41998-01-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL1-51.283SSRLBL1-5

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
13.4842.6189.90.2049.498.58707287072-384.8
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.483.5565.20.991.146.83144

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONRIGID BODY REFINEMENTTHROUGHOUT1BCC after further correction/refinement3.48188636986369255889.70.240.240.2390.284RANDOM110.4
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]
42.14-32.46-9.68
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d21.5
c_scangle_it2.53
c_mcangle_it2.43
c_scbond_it1.47
c_angle_deg1.4
c_mcbond_it1.34
c_improper_angle_d1
c_bond_d0.009
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d21.5
c_scangle_it2.53
c_mcangle_it2.43
c_scbond_it1.47
c_angle_deg1.4
c_mcbond_it1.34
c_improper_angle_d1
c_bond_d0.009
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms31820
Nucleic Acid Atoms
Solvent Atoms17
Heterogen Atoms836

Software

Software
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing