3H6V
Crystal structure of the iGluR2 ligand-binding core (S1S2J-N754S) in complex with glutamate and NS5206 at 2.10 A resolution
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1MM6 | PDB ENTRY 1MM6 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 4.5 | 279 | 20 % PEG 4000, 0.3 M Lithium sulfate, 0.1 M Phosphate-citrate pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 279K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.48 | 50.45 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 99.558 | ¦Á = 90 |
b = 122.035 | ¦Â = 90 |
c = 47.724 | ¦Ã = 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 | 96.5 | CCD | MAR CCD 165 mm | 2005-12-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | MAX II BEAMLINE I711 | MAX II | I711 |
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 | 2.1 | 24.89 | 99.9 | 0.119 | 0.119 | 4.2 | 6 | 34807 | 21.7 |
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) | ||||||||||
1 | 2.1 | 2.21 | 100 | 0.386 | 0.386 | 1.7 | 6.1 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | DIFFERENCE FOURIER | THROUGHOUT | PDB ENTRY 1MM6 | 2.1 | 23.86 | 34759 | 1735 | 99.9 | 0.188 | 0.188 | 0.228 | RANDOM | 23.3 |
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] | |
-5.056 | 4.721 | 0.335 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 22.2 |
c_scangle_it | 3.178 |
c_scbond_it | 2.167 |
c_mcangle_it | 1.973 |
c_mcbond_it | 1.297 |
c_angle_deg | 1.19 |
c_improper_angle_d | 0.77 |
c_bond_d | 0.006 |
c_bond_d_na | |
c_bond_d_prot |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4056 |
Nucleic Acid Atoms | |
Solvent Atoms | 659 |
Heterogen Atoms | 125 |
Software
Software | |
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Software Name | Purpose |
MOSFLM | data reduction |
SCALA | data scaling |
CNS | refinement |
PDB_EXTRACT | data extraction |
REFMAC | phasing |