2OD6
Crystal structure of a dimeric ferredoxin-like protein (jcvi_pep_1096682647733) from uncultured marine organism at 1.85 A resolution
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP, NANODROP | 9 | 277 | 30.0% PEG-6000, 0.1M Bicine pH 9.0, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.36 | 47.89 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 36.433 | α = 90 |
b = 92.842 | β = 90 |
c = 144.927 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | MARMOSAIC 325 mm CCD | Flat mirror (vertical focusing) | 2006-11-19 | M | MAD |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL11-1 | 0.91837, 0.97944, 0.97972 | SSRL | BL11-1 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.8 | 29.086 | 99.8 | 0.072 | 0.072 | 6.1 | 3.6 | 42961 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.85 | 1.9 | 100 | 0.611 | 0.611 | 1.2 | 3.6 | 3134 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | MAD | THROUGHOUT | 1.85 | 29.086 | 42910 | 2164 | 99.68 | 0.198 | 0.197 | 0.231 | RANDOM | 11.009 |
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] | |
4.05 | -2.58 | -1.47 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.353 |
r_dihedral_angle_3_deg | 14.267 |
r_dihedral_angle_4_deg | 13.632 |
r_scangle_it | 6.948 |
r_dihedral_angle_1_deg | 6.753 |
r_scbond_it | 5.681 |
r_mcangle_it | 3.122 |
r_mcbond_it | 2.465 |
r_angle_refined_deg | 1.681 |
r_angle_other_deg | 1.061 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3468 |
Nucleic Acid Atoms | |
Solvent Atoms | 301 |
Heterogen Atoms | 120 |
Software
Software | |
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Software Name | Purpose |
MolProbity | model building |
SOLVE | phasing |
REFMAC | refinement |
SCALA | data scaling |
PDB_EXTRACT | data extraction |
MOSFLM | data reduction |
CCP4 | data scaling |