4LZ5
Crystal structures of GLuR2 ligand-binding-domain in complex with glutamate and positive allosteric modulators
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 277 | 1 uL 7 mg/mL protein in 10 mM (S)-Glu, 10 mM HEPES, pH 7.5, 20 mM sodium chloride, 1 mM EDTA, 150 uM ligand (from 30 mM DMSO stock) + 1 uL reservoir (10% PEG8000, 0.1 M zinc acetate, 0.1 M sodium acetate, pH 5.5), crystals appeared in 3-5 days, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.46 | 50.02 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 114.751 | α = 90 |
b = 164.541 | β = 90 |
c = 47.46 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 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 QUANTUM 210 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 17-ID | 1.00 | APS | 17-ID |
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 | 1.5 | 94.072 | 98.3 | 0.071 | 14.7 | 6.1 | 141715 | -3 |
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 | 1.5 | 1.55 | 87.8 | 0.305 | 3.1 | 12503 |
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-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1LBC | 1.5 | 94.07 | 141629 | 7111 | 98.13 | 0.1708 | 0.169 | 0.203 | RANDOM | 20.4257 |
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] | |
0.11 | 0.08 | -0.18 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 31.609 |
r_dihedral_angle_4_deg | 20.099 |
r_dihedral_angle_3_deg | 13.313 |
r_dihedral_angle_1_deg | 6.303 |
r_scangle_it | 5.855 |
r_scbond_it | 4.123 |
r_mcangle_it | 2.811 |
r_angle_refined_deg | 2.676 |
r_mcbond_it | 2.233 |
r_angle_other_deg | 1.231 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6035 |
Nucleic Acid Atoms | |
Solvent Atoms | 1263 |
Heterogen Atoms | 83 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
AMoRE | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |