2FYU
Crystal structure of bovine heart mitochondrial bc1 with jg144 inhibitor
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1L0N |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.2 | 277.2 | 50 mM MOPS 7.2pH, 20 mM Ammonium acetate, 20% glycerol.Incubation with 2-5 mol excess of JG144. Precipitant 12% PEG4000, 0.5 M KCl, 0.1% DHPC; Protein:PPT ratio 1:0.57, VAPOR DIFFUSION, SITTING DROP, temperature 277.2K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.64 | 66.17 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 154.263 | α = 90 |
b = 154.263 | β = 90 |
c = 590.191 | γ = 90 |
Symmetry | |
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Space Group | I 41 2 2 |
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 | AREA DETECTOR | MARRESEARCH | 2004-07-03 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X29A | 1.0090 | NSLS | X29A |
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 | 2.26 | 50 | 86.1 | 0.056 | 17.2 | 4 | 157290 | -0.3 |
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 | 2.26 | 2.34 | 42.4 | 0.382 | 1.8 | 13582 |
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 | 1l0n | 2.26 | 40 | 157290 | 157290 | 3230 | 96.89 | 0.24916 | 0.24916 | 0.24843 | 0.28328 | RANDOM | 25.239 |
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] | |
2.36 | 2.36 | -4.71 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_1_deg | 11.115 |
r_scangle_it | 7.314 |
r_scbond_it | 5.686 |
r_mcangle_it | 2.514 |
r_angle_refined_deg | 2.063 |
r_mcbond_it | 0.592 |
r_chiral_restr | 0.2 |
r_nbd_refined | 0.117 |
r_xyhbond_nbd_refined | 0.096 |
r_symmetry_vdw_refined | 0.094 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 16477 |
Nucleic Acid Atoms | |
Solvent Atoms | 267 |
Heterogen Atoms | 156 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data reduction |
SCALEPACK | data scaling |