6E7U
Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to allosteric inhibitor 93-31
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 290 | 3.0-3.5 M sodium formate, 0.1 M HEPES, 35 mM sodium chloride, 7 mM Tris-HCl, 50 uM Ifenprodil |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.21 | 61.72 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 268.62 | α = 90 |
b = 59.595 | β = 117.1 |
c = 145.914 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 1 |
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 | PIXEL | DECTRIS EIGER X 16M | 2016-11-22 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 23-ID-B | 1.0332 | APS | 23-ID-B |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | 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 | 2.262 | 35 | 98.6 | 0.068 | 0.081 | 0.042 | 8.8 | 3.4 | 92724 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 2.27 | 2.32 | 97.3 | 1.091 | 1.315 | 0.723 | 0.472 | 3 |
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 | MOLECULAR REPLACEMENT | THROUGHOUT | 3QEL | 2.27 | 25 | 74940 | 3926 | 82.03 | 0.2041 | 0.2024 | 0.2367 | RANDOM | 39.604 |
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] | |
-0.21 | 0.56 | -0.66 | 0.2 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.99 |
r_dihedral_angle_4_deg | 22.294 |
r_dihedral_angle_3_deg | 15.718 |
r_dihedral_angle_1_deg | 8.451 |
r_angle_other_deg | 0.412 |
r_angle_refined_deg | 0.345 |
r_chiral_restr | 0.034 |
r_gen_planes_refined | 0.02 |
r_bond_refined_d | 0.005 |
r_gen_planes_other | 0.004 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 10977 |
Nucleic Acid Atoms | |
Solvent Atoms | 333 |
Heterogen Atoms | 221 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data scaling |
PDB_EXTRACT | data extraction |
DENZO | data reduction |
PHASER | phasing |