7VQP
Vitamin D receptor complexed with a lithocholic acid derivative
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2ZLC |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 297 | 0.1 M MOPS-NaOH, 0.1-0.4 M sodium formate, 12-22% (w/v) PEG4000, 5% (v/v) ethylene glycol |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.86 | 34.04 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 157.805 | α = 90 |
b = 37.581 | β = 98.59 |
c = 40.913 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 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 | 2021-02-23 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE BL-17A | 0.9800 | Photon Factory | BL-17A |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym I (Observed) | 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 | 1.94 | 40 | 98.4 | 0.056 | 0.999 | 8.6 | 3.4 | 17530 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.94 | 2.01 | 98.2 | 0.567 | 0.876 | 1.7 | 3.5 |
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 (All) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 2ZLC | 1.94 | 40 | 17523 | 848 | 98.058 | 0.209 | 0.207 | 0.2424 | 33.815 |
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] | |
0.109 | -0.06 | -0.11 | 0.018 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.268 |
r_dihedral_angle_4_deg | 16.235 |
r_dihedral_angle_3_deg | 15.375 |
r_lrange_it | 6.69 |
r_lrange_other | 6.688 |
r_dihedral_angle_1_deg | 5.581 |
r_scangle_it | 5.176 |
r_scangle_other | 5.174 |
r_mcangle_it | 3.692 |
r_mcangle_other | 3.691 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1927 |
Nucleic Acid Atoms | |
Solvent Atoms | 10 |
Heterogen Atoms | 36 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XDS | data scaling |
PHASER | phasing |