3SFE
crystal structure of porcine mitochondrial respiratory complex II bound with oxaloacetate and thiabendazole
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1ZOY | PDB ENTRY 1ZOY |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.2 | 290 | 0.5% n-nonyl-D-maltoside, 1.7mM n-decyl-D-maltoside, 25mM HEPES, 5% PEG 4000, 3% 1,6-hexanediol, 100mM NaCl, 10mM CaCl2, 200mM sucrose, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.51 | 65.01 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 70.71 | α = 90 |
b = 83.42 | β = 90 |
c = 294.01 | 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 315 | 2008-11-22 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE BL-17A | 1.000 | Photon Factory | BL-17A |
Data Collection
Overall | |||||||||||||||||||
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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 | 2.8 | 50 | 94.6 | 0.1 | 12 | 4.5 | 43960 | 41586 | -1 | 63.2 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 2.8 | 2.87 | 81.2 | 0.427 | 1.7 | 3.5 | 2859 |
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 | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1ZOY | 2.81 | 50 | 41586 | 32353 | 1717 | 78.06 | 0.274 | 0.21684 | 0.21405 | 0.26985 | RANDOM | 56.462 |
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] | |
1.07 | -1.68 | 0.61 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.834 |
r_dihedral_angle_3_deg | 18.752 |
r_dihedral_angle_4_deg | 14.696 |
r_dihedral_angle_1_deg | 5.374 |
r_angle_refined_deg | 1.243 |
r_scangle_it | 1.019 |
r_mcangle_it | 0.608 |
r_scbond_it | 0.58 |
r_mcbond_it | 0.327 |
r_chiral_restr | 0.074 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 8489 |
Nucleic Acid Atoms | |
Solvent Atoms | 52 |
Heterogen Atoms | 138 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data collection |
PHASES | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |