3H6U
Crystal structure of the iGluR2 ligand-binding core (S1S2J-N754S) in complex with glutamate and NS1493 at 1.85 A resolution
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1M5C | PDB ENTRY 1M5C |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | 4.5 | 279 | 25 % PEG 8000, 0.1 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 |
2.29 | 46.4 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 88.462 | ¦Á = 90 |
b = 64.086 | ¦Â = 90 |
c = 47.272 | ¦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 | 100 | CCD | MARRESEARCH | 2006-02-03 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | EMBL/DESY, HAMBURG BEAMLINE X11 | EMBL/DESY, HAMBURG | X11 |
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 | 1.85 | 19.47 | 98.7 | 0.058 | 33.1 | 7.9 | 24228 | 21 |
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 | 1.85 | 1.92 | 91.6 | 0.419 | 0.419 | 5.2 | 7.9 |
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 1M5C | 1.85 | 19.47 | 23457 | 1177 | 99.4 | 0.181 | 0.181 | 0.215 | RANDOM | 24.8 |
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] | |
-11.136 | 4.687 | 6.449 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 21.9 |
c_scangle_it | 3.14 |
c_scbond_it | 2.111 |
c_mcangle_it | 1.814 |
c_mcbond_it | 1.232 |
c_angle_deg | 1.21 |
c_improper_angle_d | 0.71 |
c_bond_d | 0.005 |
c_bond_d_na | |
c_bond_d_prot |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2037 |
Nucleic Acid Atoms | |
Solvent Atoms | 384 |
Heterogen Atoms | 93 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
CNS | refinement |
PDB_EXTRACT | data extraction |
REFMAC | phasing |