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) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1BCC | 1BCC after further correction/refinement |
Crystallization
Crystalization Experiments | ||||
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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 | |
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Matthews coefficient | Solvent content |
4.06 | 69.74 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 171.717 | α = 90 |
b = 181.297 | β = 90 |
c = 241.288 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
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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 | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL1-5 | 1.283 | SSRL | BL1-5 |
Data Collection
Overall | |||||||||||||||||||
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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 | |||||||||||||||||||
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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 | |||||||||||||||||||
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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 | R-Free | 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 | 0.284 | RANDOM | 110.4 |
Temperature Factor Modeling | ||||||
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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 | |
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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 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 31820 |
Nucleic Acid Atoms | |
Solvent Atoms | 17 |
Heterogen Atoms | 836 |
Software
Software | |
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Software Name | Purpose |
CNS | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
CNS | phasing |