8IGV
Hexameric Ring Complex of Engineered V1-ATPase bound to 5 ADPs: A3(De)3_(ADP-Pi)1cat(ADP)2cat,2non-cat
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 8IGU |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | 0.1 M Tris-HCl (pH 8.5), 24% PEG 3350, 0.2 M Ammonium Acetate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.67 | 53.89 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 119.667 | α = 90 |
b = 126.736 | β = 93.934 |
c = 123.649 | 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 | PIXEL | DECTRIS EIGER X 4M | 2018-03-10 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE BL-1A | 1.1 | Photon Factory | BL-1A |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | CC (Half) | 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 | 3.15 | 48.38 | 100 | 0.21 | 0.087 | 0.984 | 7.7 | 7.1 | 63835 | 55.73 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 3.15 | 3.23 | 1.11 | 0.49 | 0.569 | 2 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 3.15 | 48.38 | 1.34 | 63799 | 3152 | 99.97 | 0.214 | 0.2113 | 0.2106 | 0.2681 | 0.267 | 56.31 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 23.2046 |
f_angle_d | 0.9392 |
f_chiral_restr | 0.056 |
f_plane_restr | 0.0057 |
f_bond_d | 0.0049 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 23997 |
Nucleic Acid Atoms | |
Solvent Atoms | 117 |
Heterogen Atoms | 145 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
Aimless | data scaling |
PHASER | phasing |
XDS | data reduction |