3H6W
Crystal structure of the iGluR2 ligand-binding core (S1S2J-N754S) in complex with glutamate and NS5217 at 1.50 A resolution
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 1FTJ | PDB entry 1FTJ |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 279 | 20 % PEG 4000, 0.1 M Ammonium sulfate, 0.1 M Cacodylate pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 279K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.25 | 45.28 |
Crystal Data
Unit Cell | |
---|---|
Length ( ? ) | Angle ( ? ) |
a = 47.01 | ¦Á = 90 |
b = 47.179 | ¦Â = 91.88 |
c = 118.412 | ¦Ã = 90 |
Symmetry | |
---|---|
Space Group | P 1 2 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | MAR CCD 165 mm | 2006-09-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | EMBL/DESY, HAMBURG BEAMLINE X13 | 0.8080 | EMBL/DESY, HAMBURG | X13 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.49 | 17.38 | 85.6 | 0.041 | 0.041 | 25.2 | 3.7 | 72325 | 18 |
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 | 1.49 | 1.55 | 95.4 | 0.405 | 0.405 | 2.6 | 8047 |
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-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB entry 1FTJ | 1.49 | 17.38 | 71603 | 1392 | 84.51 | 0.189 | 0.232 | RANDOM | 19.9 |
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] | |
0.76 | 0.84 | -1.33 | 0.62 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.659 |
r_dihedral_angle_4_deg | 21.63 |
r_dihedral_angle_3_deg | 13.571 |
r_dihedral_angle_1_deg | 5.768 |
r_sphericity_free | 4.937 |
r_scangle_it | 2.987 |
r_scbond_it | 2.235 |
r_sphericity_bonded | 2.065 |
r_mcangle_it | 1.44 |
r_angle_refined_deg | 1.36 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 4081 |
Nucleic Acid Atoms | |
Solvent Atoms | 683 |
Heterogen Atoms | 96 |
Software
Software | |
---|---|
Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
MAR345dtb | data collection |