1QKM
HUMAN OESTROGEN RECEPTOR BETA LIGAND-BINDING DOMAIN IN COMPLEX WITH PARTIAL AGONIST GENISTEIN
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1ERE | PDB ENTRY 1ERE |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 8.1 | 6-9% (W/V) PEG 6000, 1.6-2.1M NACL, 0.1M TRIS-HCL, PH 8.1 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.44 | 49 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 63.12 | α = 90 |
b = 63.12 | β = 90 |
c = 250.23 | γ = 120 |
Symmetry | |
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Space Group | P 61 2 2 |
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 CCD | 1998-12-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID14-4 | ESRF | ID14-4 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.8 | 60 | 99.7 | 0.049 | 15 | 8 | 28523 | -3 | 32.6 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.8 | 1.83 | 100 | 0.433 | 4 | 8 |
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 | THROUGHOUT | PDB ENTRY 1ERE | 1.8 | 55 | 28460 | 1441 | 99.7 | 0.215 | 0.252 | RANDOM | 41.3 |
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] | |
3.115 | -1.138 | 3.116 | -3.827 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
p_transverse_tor | 23.7 |
p_staggered_tor | 16.1 |
p_scangle_it | 3.745 |
p_mcangle_it | 2.847 |
p_planar_tor | 2.6 |
p_scbond_it | 2.359 |
p_mcbond_it | 1.851 |
p_multtor_nbd | 0.361 |
p_singtor_nbd | 0.181 |
p_chiral_restr | 0.137 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1781 |
Nucleic Acid Atoms | |
Solvent Atoms | 139 |
Heterogen Atoms | 20 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
AMoRE | phasing |