4IX9
Crystal structure of subunit F of V-ATPase from S. cerevisiae
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8.8 | 291 | 30% PEG 4000, 0.05M MgCl2,6H2O, 0.1M Tris HCl pH 8.8, 10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.25 | 45.29 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 47.146 | α = 90 |
b = 160.312 | β = 90 |
c = 102.429 | γ = 90 |
Symmetry | |
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Space Group | C 2 2 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 | ADSC QUANTUM 315 | Vertically Collimating Premirror, Toroidal Focusing Mirror | 2012-03-31 | M | MAD |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSRRC BEAMLINE BL13B1 | 0.978836, 0.978683, 0.963626 | NSRRC | BL13B1 |
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 | 2.33 | 50 | 99.5 | 0.084 | 18.8 | 6.5 | 17114 | 17018 | 2 | 2 | 37.6 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.33 | 2.41 | 96.7 | 0.434 | 2.2 | 4.6 | 1612 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | 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 | MAD | THROUGHOUT | 2.33 | 26.53 | 15276 | 16138 | 862 | 99.44 | 0.15523 | 0.1522 | 0.21154 | RANDOM | 39.034 |
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] | |
-0.65 | -0.28 | 0.93 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 39.684 |
r_dihedral_angle_3_deg | 19.625 |
r_dihedral_angle_4_deg | 15.753 |
r_dihedral_angle_1_deg | 7.231 |
r_angle_refined_deg | 1.792 |
r_chiral_restr | 0.117 |
r_bond_refined_d | 0.015 |
r_gen_planes_refined | 0.007 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2934 |
Nucleic Acid Atoms | |
Solvent Atoms | 245 |
Heterogen Atoms | 62 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data collection |
SHELX | model building |
SHELXD | phasing |
SHELXE | model building |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
SHELX | phasing |