3FKS
Yeast F1 ATPase in the absence of bound nucleotides
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1W0J | PDB entry 1W0J |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.3 | 277 | 6.25% PEG 6000, 10% Glycerol, 4% Methanol, 0.05M Sodium acetate, 0.5mM Nickel sulfate, 2 mM Sodium pyrophosphate, 2mM Magnesium chloride, pH 7.3, VAPOR DIFFUSION, SITTING DROP, temperature 277.0K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.7 | 54.49 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 111.934 | α = 90 |
b = 290.487 | β = 101.75 |
c = 188.7 | 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 300 mm CCD | 2006-02-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 22-ID | 1.0000 | APS | 22-ID |
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 | 3.587 | 50 | 98 | 0.094 | 9 | 2.8 | 134821 | 134821 | -1 | 111.6 |
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) | |||||||||||
3.587 | 3.69 | 98 | 0.423 | 1.6 | 2.8 |
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 (All) | 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 1W0J | 3.587 | 33.203 | 1.34 | 134821 | 134790 | 2727 | 98.11 | 0.2435 | 0.2422 | 0.3062 | RANDOM |
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] | |
6.0236 | -4.5563 | 2.5638 | -8.5874 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_angle_d | 0.8 |
f_bond_d | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 71719 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 75 |
Software
Software | |
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Software Name | Purpose |
MAR345 | data collection |
PHASER | phasing |
PHENIX | refinement |
X-GEN | data reduction |
X-GEN | data scaling |