3X36
Crystal structure of the human vitamin D receptor ligand binding domain complexed with 7,8-cis-1a,25-Dihydroxy-19-norvitamin D3
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 6.5 | 293 | 0.1M MES, pH6.5, 1.2-1.6M ammonium sulfate, VAPOR DIFFUSION, temperature 293.0K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.55 | 51.71 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 44.819 | α = 90 |
b = 51.27 | β = 90 |
c = 132.166 | 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 | CCD | ADSC QUANTUM 315r | 2013-07-28 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | AUSTRALIAN SYNCHROTRON BEAMLINE MX2 | 0.95370 | Australian Synchrotron | MX2 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.93 | 47.8 | 78.2 | 2 | 1 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1 | 1.93 | 2.03 | 24.8 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.93 | 42.48 | 17506 | 939 | 78.01 | 0.17918 | 0.1769 | 0.22129 | RANDOM | 18.734 |
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] | |
-0.55 | -0.38 | 0.93 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.625 |
r_dihedral_angle_4_deg | 19.651 |
r_dihedral_angle_3_deg | 17.272 |
r_dihedral_angle_1_deg | 6.946 |
r_angle_refined_deg | 2.116 |
r_angle_other_deg | 1.004 |
r_chiral_restr | 0.129 |
r_bond_refined_d | 0.018 |
r_gen_planes_refined | 0.01 |
r_gen_planes_other | 0.002 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2022 |
Nucleic Acid Atoms | |
Solvent Atoms | 131 |
Heterogen Atoms | 29 |
Software
Software | |
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Software Name | Purpose |
XDS | data scaling |
MOLREP | phasing |
REFMAC | refinement |
XDS | data reduction |
SCALA | data scaling |