3FOO
A Triangular Cytochrome b562 Superstructure Mediated by Ni Coordination - Monoclinic Form
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2QLA | PDB entry 2QLA |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 293 | 25% PEG2000, 0.2 M NaCl, 0.1 M TRIS, 3.3 mM NiCl2, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.68 | 54.15 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 70.339 | ¦Á = 90 |
b = 107.396 | ¦Â = 105.52 |
c = 102.051 | ¦Ã = 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 | CCD | ADSC QUANTUM 315 | Vertical focusing mirror; single crystal Si(311) bent monochromator (horizontal focusing) | 2008-08-04 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL9-1 | 0.97607 | SSRL | BL9-1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 2.4 | 98.533 | 97.2 | 0.096 | 0.096 | 6.464 | 2.7 | 56311 | 55485 | 2 | 2 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.4 | 2.53 | 97 | 0.552 | 0.552 | 1.3 | 2.6 | 8079 |
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 | THROUGHOUT | PDB entry 2QLA | 2.4 | 98.53 | 57214 | 55103 | 3980 | 96.31 | 0.213 | 0.213 | 0.209 | 0.268 | RANDOM | 41.455 |
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] | |
0.1 | 0.11 | -0.15 | 0.11 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 43.25 |
r_dihedral_angle_3_deg | 19.263 |
r_dihedral_angle_4_deg | 13.467 |
r_dihedral_angle_1_deg | 5.06 |
r_scangle_it | 1.714 |
r_angle_refined_deg | 1.246 |
r_scbond_it | 1.142 |
r_mcangle_it | 0.63 |
r_mcbond_it | 0.37 |
r_nbtor_other | 0.324 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 9648 |
Nucleic Acid Atoms | |
Solvent Atoms | 119 |
Heterogen Atoms | 756 |
Software
Software | |
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Software Name | Purpose |
MOSFLM | data reduction |
SCALA | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
ADSC | data collection |
MOLREP | phasing |