3D89
Crystal Structure of a Soluble Rieske Ferredoxin from Mus musculus
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6 | 293 | Protein Solution (~15 mg/ml native protein, 0.025 M NaCl, 0.005 M MOPS pH 7.0) mixed in a 1:1 ratio with Well Solution ( 25% MEPEG 5K, 0.12 M Trisodium citrate, 0.10 M MES ph 6.0) Cryoprotected with 15% ethylene glycol; Mercury derivative crystal soaked overnight in in mother liquor containing 0.002 M thimersol, vapor diffusion, hanging drop, temperature 293K, VAPOR DIFFUSION, HANGING DROP |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.1 | 40.5 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 52.413 | α = 90 |
b = 52.413 | β = 90 |
c = 108.808 | γ = 90 |
Symmetry | |
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Space Group | P 43 21 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 | CCD | MARMOSAIC 300 mm CCD | Adjustable focus K-B pair Si plus Pt, Rh coatings | 2007-07-06 | M | SINGLE WAVELENGTH | |||||
2 | 1 | x-ray | 100 | CCD | MARMOSAIC 225 mm CCD | Rosenbaum-Rock vertical focusing mirror | 2007-06-11 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 23-ID-B | 0.96419 | APS | 23-ID-B |
2 | SYNCHROTRON | APS BEAMLINE 22-BM | 1.000 | APS | 22-BM |
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 | 2.07 | 50 | 99.4 | 0.057 | 18.354 | 12.7 | 9806 |
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 | 2.07 | 2.14 | 95.5 | 0.621 | 1.845 | 7.1 | 900 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | SAD | THROUGHOUT | 2.071 | 37.75 | 9754 | 472 | 99.399 | 0.2 | 0.199 | 0.228 | RANDOM | 46.027 |
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] | |
0.148 | 0.148 | -0.295 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.566 |
r_dihedral_angle_3_deg | 15.863 |
r_dihedral_angle_4_deg | 14 |
r_dihedral_angle_1_deg | 6.528 |
r_scangle_it | 3.12 |
r_scbond_it | 2.169 |
r_angle_refined_deg | 1.848 |
r_mcangle_it | 1.486 |
r_mcbond_it | 1.018 |
r_nbtor_refined | 0.306 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1099 |
Nucleic Acid Atoms | |
Solvent Atoms | 48 |
Heterogen Atoms | 8 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
SHARP | phasing |
DM | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |