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Chicken cytochrome BC1 complex with ZN++ and an iodinated derivative of kresoxim-methyl bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BCC 1BCC after further correction/refinement
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.7 277 20MM 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 coefficient Solvent content 4.06 69.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 171.717 α = 90 b = 181.297 β = 90 c = 241.288 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 100 CCD ADSC QUANTUM 4 1998-01-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL1-5 1.283 SSRL BL1-5
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 3.48 42.61 89.9 0.204 9.49 8.5 87072 87072 -3 84.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.48 3.55 65.2 0.99 1.14 6.8 3144
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 RIGID BODY REFINEMENT THROUGHOUT 1BCC after further correction/refinement 3.48 18 86369 86369 2558 89.7 0.24 0.24 0.239 0.232 0.284 0.2765 RANDOM 110.4
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 Key Refinement Restraint Deviation c_dihedral_angle_d 21.5 c_scangle_it 2.53 c_mcangle_it 2.43 c_scbond_it 1.47 c_angle_deg 1.4 c_mcbond_it 1.34 c_improper_angle_d 1 c_bond_d 0.009 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.5 c_scangle_it 2.53 c_mcangle_it 2.43 c_scbond_it 1.47 c_angle_deg 1.4 c_mcbond_it 1.34 c_improper_angle_d 1 c_bond_d 0.009 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 Atoms Number Protein Atoms 31820 Nucleic Acid Atoms Solvent Atoms 17 Heterogen Atoms 836
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling CNS phasing