1ZRT
Rhodobacter capsulatus cytochrome bc1 complex with stigmatellin bound
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2BCC | PDB ENTRY 2BCC |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.2 | 277 | PEG-400, 0.1 M MgCl2, Heptanetriol, Cacodylate, Undecylmaltoside |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.56 | 65.16 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 95.633 | α = 90 |
b = 154.36 | β = 113.57 |
c = 103.057 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
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 | IMAGE PLATE | MAR scanner 345 mm plate | 2001-03-14 | M | SINGLE WAVELENGTH | ||||||
2 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 4 | 2001-03-20 | M | SINGLE WAVELENGTH | ||||||
3 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 4 | 2001-03-21 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL7-1 | 1.0800 | SSRL | BL7-1 |
2 | SYNCHROTRON | ALS BEAMLINE 5.0.2 | 1.10 | ALS | 5.0.2 |
3 | SYNCHROTRON | ALS BEAMLINE 5.0.2 | 1.10 | ALS | 5.0.2 |
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 | 3.5 | 60 | 97.6 | 0.12 | 8.5 | 2.68 | 33596 | -999.9 | -3 | 100.43 |
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) | |||||||||||
3.5 | 3.63 | 94 | 0.28 | 3.9 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | 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 | FREE R-VALUE | PDB ENTRY 2BCC | 3.51 | 59.77 | 1.35 | 33205 | 1656 | 96.46 | 0.224 | 0.2207 | 0.2887 | RANDOM | 119.7 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 21.5362 |
f_angle_d | 2.187 |
f_chiral_restr | 0.0852 |
f_bond_d | 0.0187 |
f_plane_restr | 0.0118 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 13482 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 419 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
CNS | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
AMoRE | phasing |