3W5T
Crystal structure of complexes of vitamin D receptor ligand binding domain with lithocholic acid derivatives
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1RJK | PDB ENTRY 1RJK |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 291.5 | 0.1M 3-(N-morpholino) propanesulfonic acid/sodium hydroxide, 0.1-0.4M sodium formate, 12-22% PEG 4000, 0-10% ethylene glycol , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291.5K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.08 | 40.76 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 154.485 | α = 90 |
b = 41.791 | β = 96.32 |
c = 41.63 | 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 | 95 | CCD | ADSC QUANTUM 4r | 2006-11-07 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE BL-6A | 0.978 | Photon Factory | BL-6A |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (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 | 2.2 | 50 | 99.6 | 0.045 | 0.045 | 30.3 | 3.6 | 11996 | 29.1 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.2 | 2.28 | 96.8 | 0.357 | 0.357 | 3.9 | 3.5 | 1145 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 | PDB ENTRY 1RJK | 2.29 | 40.33 | 12416 | 11258 | 1158 | 93.2 | 0.211 | 0.211 | 0.265 | RANDOM |
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] | |
-16.26 | -4.62 | 17.85 | -1.59 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 19.2 |
c_scangle_it | 3 |
c_mcangle_it | 2.69 |
c_scbond_it | 2.07 |
c_mcbond_it | 1.59 |
c_angle_deg | 1.2 |
c_improper_angle_d | 0.84 |
c_bond_d | 0.007 |
c_bond_d_na | |
c_bond_d_prot |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2032 |
Nucleic Acid Atoms | |
Solvent Atoms | 56 |
Heterogen Atoms | 31 |
Software
Software | |
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Software Name | Purpose |
SERGUI | data collection |
CNS | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
CNS | phasing |