5XPL
Crystal structure of VDR-LBD complexed with 22S-butyl-25-hydroxyphenyl-2-methylidene-19,26,27-trinor-25-oxo-1-hydroxyvitamin D3
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 293 | MOPS-Na, Na-Formate, PEG 4000, Ethylenglycol |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.04 | 39.72 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 128.78 | α = 90 |
b = 44.91 | β = 93.62 |
c = 45.52 | 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 PILATUS3 S 6M | 2016-02-29 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE BL-17A | 1.0000 | Photon Factory | BL-17A |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 2.05 | 64.26 | 88.7 | 11.3 | 2.9 | 14660 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | 2.05 | 64.26 | 13899 | 748 | 88.69 | 0.18883 | 0.18607 | 0.24173 | RANDOM | 26.443 |
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] | |
-0.87 | -0.04 | 0.79 | 0.09 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.433 |
r_dihedral_angle_3_deg | 16.921 |
r_dihedral_angle_4_deg | 12.899 |
r_long_range_B_refined | 6.378 |
r_long_range_B_other | 6.369 |
r_dihedral_angle_1_deg | 5.173 |
r_scangle_other | 4.773 |
r_mcangle_it | 3.646 |
r_mcangle_other | 3.645 |
r_scbond_it | 3.138 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1982 |
Nucleic Acid Atoms | |
Solvent Atoms | 91 |
Heterogen Atoms | 39 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |