4YTP
CRYSTAL STRUCTURE OF PORCINE HEART MITOCHONDRIAL COMPLEX II BOUND WITH N-[(4-tert-butylphenyl)methyl]-2-(trifluoromethyl)benzamide
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1ZOY |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.4 | 293 | 5MM HEPES-NAOH, 7% PEG 4000, 200MM SUCROSE, 100MM NACL, 10MM CACL2, 0.5MM EDTA, 3% 1,6-HAXANEDIOL,0.5% N-DECYL-BETA-D-MALTOSIDE |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.16 | 61.03 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 71.429 | ¦Á = 90 |
b = 84.008 | ¦Â = 90 |
c = 294.817 | ¦Ã = 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 270 | 2013-11-09 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE BL-17A | 0.98000 | 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 | 3.1 | 50 | 93.3 | 0.095 | 11.4 | 3.9 | 31105 |
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 | 3.1 | 3.15 | 94.9 | 0.516 | 1.7 | 4.6 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 1ZOY | 3.1 | 20 | 25461 | 1352 | 80.74 | 0.20954 | 0.20638 | 0.26903 | RANDOM | 70.325 |
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] | |
2.55 | -1.16 | -1.39 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.755 |
r_dihedral_angle_3_deg | 18.588 |
r_dihedral_angle_4_deg | 18.389 |
r_dihedral_angle_1_deg | 6.33 |
r_angle_refined_deg | 1.227 |
r_angle_other_deg | 0.838 |
r_chiral_restr | 0.065 |
r_bond_refined_d | 0.007 |
r_gen_planes_refined | 0.004 |
r_gen_planes_other | 0.002 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 8480 |
Nucleic Acid Atoms | |
Solvent Atoms | 22 |
Heterogen Atoms | 139 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data processing |
HKL-2000 | data scaling |
MOLREP | phasing |