3K1A
Insights into substrate binding at FeMo-cofactor in nitrogenase from the structure of an alpha-70Ile MoFe protein variant
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | LIQUID DIFFUSION | 8 | 298 | 30% PEG 4000, 100mM Tris-HCl pH 8.0, 170-190mM Sodium molybdate and 1mM Dithionite, LIQUID DIFFUSION, temperature 298.0K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.2 | 44.12 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 77.019 | α = 90 |
b = 129.458 | β = 109.01 |
c = 107.088 | 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 | CCD | MARMOSAIC 325 mm CCD | mirrors | 2008-07-21 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL11-1 | 0.8900 | SSRL | BL11-1 |
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 | 2.23 | 50 | 99.9 | 0.115 | 11.8 | 3.8 | 187881 | 2.3 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
2.23 | 2.33 | 0.233 | 3.5 | 18797 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | PDB entry 2MIN | 2.23 | 50 | 90665 | 4778 | 98.46 | 0.207 | 0.20449 | 0.25433 | RANDOM | 31.399 |
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] | |
1.66 | 0.38 | 0.23 | -1.65 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.469 |
r_dihedral_angle_4_deg | 24.593 |
r_dihedral_angle_3_deg | 15.597 |
r_scangle_it | 7.743 |
r_dihedral_angle_1_deg | 5.811 |
r_scbond_it | 5.386 |
r_angle_refined_deg | 3.226 |
r_mcbond_it | 2.29 |
r_mcangle_it | 2.138 |
r_angle_other_deg | 1.279 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 15778 |
Nucleic Acid Atoms | |
Solvent Atoms | 830 |
Heterogen Atoms | 96 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data collection |
PHASER | phasing |
REFMAC | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |