3V49
Structure of ar lbd with activator peptide and sarm inhibitor 1
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2AMA | PDB ENTRY 2AMA |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 7.5 | 291 | Hanging drop set up as a 50:50 mixture of 1 microL protein+1 microL reservoir with: A) protein solution = 80 microL hAR LBD (3.5 mg/ml) + 1.5 microL activator undecapeptide (GAFQNLFQSVR)+1 microL LiSO4 (0.2 M) in HEPES buffer 0.1 M + 0.5 mg inhibitor 1 (PK0) B) Reservoir = 1 ml HEPES buffer 0.1 M + PEG 4000 12-20 %, pH 7.5, VAPOR DIFFUSION, temperature 291K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.84 | 38.18 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 54.629 | α = 90 |
b = 67.331 | β = 90 |
c = 69.809 | 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 | 2007-12-12 | M | SINGLE WAVELENGTH | ||||||
2 | 1 | x-ray | 100 | 2008-01-10 | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE BM30A | ESRF | BM30A | |
2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 1.7 | 34.9 | 98.3 | 0.043 | 29.6 | 4.5 | 28211 | 4 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.7 | 1.8 | 97.6 | 0.185 | 6.5 | 4 |
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 (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | FOURIER SYNTHESIS | THROUGHOUT | PDB ENTRY 2AMA | 1.7 | 34 | 28377 | 97.9 | 0.193 | 0.185 |
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] | |
Coordinate Error | ||
---|---|---|
Structure Solution Method | Refinement High Resolution | Refinement Low Resolution |
7 | 2362 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
s_zero_chiral_vol | 0.085 |
s_similar_adp_cmpnt | 0.071 |
s_non_zero_chiral_vol | 0.046 |
s_angle_d | 0.033 |
s_from_restr_planes | 0.025 |
s_anti_bump_dis_restr | 0.023 |
s_bond_d | 0.011 |
s_similar_dist | |
s_rigid_bond_adp_cmpnt | |
s_approx_iso_adps |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2084 |
Nucleic Acid Atoms | |
Solvent Atoms | 238 |
Heterogen Atoms | 33 |
Software
Software | |
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Software Name | Purpose |
ADSC | data collection |
SHELX | model building |
SHELXL-97 | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
SHELX | phasing |