8IQN
Crystal structure of the human vitamin D receptor ligand binding domain complexed with 24,24-F2-25(OH)D3
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 293 | 0.1M MES, pH6.5, 1.2-1.6M ammonium sulfate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.23 | 44.78 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 45.02 | α = 90 |
b = 51.434 | β = 90 |
c = 132.375 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 PILATUS 6M | 2022-10-09 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SPRING-8 BEAMLINE BL45XU | 1.0 | SPring-8 | BL45XU |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.639 | 47.988 | 96.3 | 0.826 | 17.19 | 1.74 | 64231 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.745 | 1.78 | 0.826 |
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 (All) | R-Work | R-Free | Mean Isotropic B | ||||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 1.639 | 47.988 | 36808 | 1844 | 95.269 | 0.182 | 0.1812 | 0.206 | 17.917 |
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] | |
-0.013 | 0.014 | -0.001 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_6_deg | 16.444 |
r_dihedral_angle_3_deg | 14.682 |
r_dihedral_angle_2_deg | 8.167 |
r_lrange_it | 7.041 |
r_lrange_other | 7.039 |
r_scangle_it | 5.583 |
r_scangle_other | 5.582 |
r_dihedral_angle_1_deg | 5.163 |
r_scbond_it | 3.614 |
r_scbond_other | 3.612 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2023 |
Nucleic Acid Atoms | |
Solvent Atoms | 117 |
Heterogen Atoms | 31 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XDS | data scaling |
MOLREP | phasing |