6HXH
Structure of the human ATP citrate lyase holoenzyme in complex with citrate, coenzyme A and Mg.ADP
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 6HXI |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.15 | 293 | 13.5% PEG3350 0.2 M Na2HPO4 pH 8.15 Protein sample buffer: 20 mM citrate pH 6.0 10 mM CoASH 50 mM Mg.ADP |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.41 | 63.96 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 150.364 | α = 91.53 |
b = 154.011 | β = 110.04 |
c = 154.087 | γ = 107.46 |
Symmetry | |
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Space Group | P 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 16M | 2017-12-10 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X06SA | 0.999977 | SLS | X06SA |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | Rrim 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 | 3.3 | 48.46 | 95.4 | 0.201 | 0.997 | 8.38 | 7.5 | 1319341 | 176777 | 105.25 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 3.3 | 3.38 | 95.7 | 2.8 | 0.283 | 0.77 | 7.6 |
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 | 6hxi | 3.3 | 48.46 | 176285 | 8667 | 95.6 | 0.157 | 0.156 | 0.187 | RANDOM | 127.4 |
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] | |
-4.4302 | 1.8242 | 3.0565 | 16.1118 | 10.9122 | -11.6816 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
t_other_torsion | 19.32 |
t_omega_torsion | 2.83 |
t_angle_deg | 1.16 |
t_bond_d | 0.01 |
t_dihedral_angle_d | |
t_incorr_chiral_ct | |
t_pseud_angle | |
t_trig_c_planes | |
t_gen_planes | |
t_it |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 64032 |
Nucleic Acid Atoms | |
Solvent Atoms | 16 |
Heterogen Atoms | 760 |
Software
Software | |
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Software Name | Purpose |
BUSTER | refinement |
XDS | data reduction |
Aimless | data scaling |
PHASER | phasing |