1YA3
Crystal structure of the human mineralocorticoid receptor ligand-binding domain bound to progesterone and harboring the S810L mutation responsible for a severe form of hypertension
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1Y9R | pdb entry 1Y9R |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.8 | 297 | PEG 4000, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 297K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.22 | 44.04 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 120.7237 | ¦Á = 90 |
b = 120.7237 | ¦Â = 90 |
c = 42.5081 | ¦Ã = 120 |
Symmetry | |
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Space Group | P 31 |
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 | 80 | CCD | MARRESEARCH | MIRRORS | 2004-11-21 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE BM30A | 0.97950 | ESRF | BM30A |
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 | 2.34 | 18.73 | 81.7 | 0.076 | 0.063 | 8.6 | 2.5 | 23880 | 22222 | 22.4 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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) | ||||||||||
2.34 | 2.47 | 80.3 | 0.311 | 0.372 | 2.8 | 2.4 | 3446 |
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 (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | pdb entry 1Y9R | 2.34 | 18.72 | 22222 | 22222 | 2227 | 81.7 | 0.252 | 0.252 | 0.237 | 0.284 | RANDOM | 48.6 |
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] | |
-1.7929 | -0.8964 | -1.7929 | 9.4578 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 20.8 |
c_angle_deg | 1.4 |
c_improper_angle_d | 0.84 |
c_bond_d | 0.015 |
c_bond_d_na | |
c_bond_d_prot | |
c_angle_d | |
c_angle_d_na | |
c_angle_d_prot | |
c_angle_deg_na |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5638 |
Nucleic Acid Atoms | |
Solvent Atoms | 57 |
Heterogen Atoms | 69 |
Software
Software | |
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Software Name | Purpose |
MOSFLM | data reduction |
SCALA | data scaling |
BEAST | model building |
CNS | refinement |
CCP4 | data scaling |
BEAST | phasing |