4YNK
Crystal structure of vitamin D receptor ligand binding domain complexed with a 19-norvitamin D compound
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 293.15 | MOPS, Sodium Formate, PEG4000, Ethylene glycol |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.85 | 33.6 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 157.437 | α = 90 |
b = 37.29 | β = 98.47 |
c = 41.121 | 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 | CCD | ADSC QUANTUM 315 | 2014-04-21 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SPRING-8 BEAMLINE BL38B1 | 1.0 | SPring-8 | BL38B1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | 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 | 2.2 | 50 | 99.7 | 0.128 | 0.151 | 0.08 | 7.3 | 3.5 | 12259 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 2.2 | 2.24 | 99.8 | 0.679 | 0.806 | 0.43 | 0.74 | 3.4 | 596 |
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-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 2ZL9 | 2.3 | 50 | 9962 | 1039 | 92.8 | 0.2015 | 0.2571 | Random | 37.7062 |
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] | |
-17.414 | -1.723 | 4.863 | 12.552 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_scangle_it | 3.044 |
c_mcangle_it | 2.242 |
c_scbond_it | 2.091 |
c_mcbond_it | 1.373 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2009 |
Nucleic Acid Atoms | |
Solvent Atoms | 47 |
Heterogen Atoms | 37 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data scaling |
CNS | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data reduction |
CNS | phasing |