3GBB
X-ray structure of iGluR5 ligand-binding core (S1S2) in complex with MSVIII-19 at 2.10A resolution
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1YCJ |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 4.5 | 280 | PEG4000, LiSO4, phosphate-citrate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 280K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.28 | 46 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 44.9 | α = 100.89 |
b = 45.12 | β = 92.31 |
c = 66.98 | γ = 94.65 |
Symmetry | |
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Space Group | P 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 | 110 | CCD | MAR CCD 165 mm | 2006-05-26 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | MAX II BEAMLINE I911-2 | 1.043 | MAX II | I911-2 |
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 | 65.668 | 96.4 | 0.081 | 0.081 | 8.511 | 2.2 | 28932 | 28932 | 12.2 |
Highest Resolution Shell | |||||||||||||||||||
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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) | ||||||||||
2.1 | 2.21 | 94.5 | 0.271 | 0.271 | 2.8 | 2.2 | 4160 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 | 1YCJ | 2.1 | 29.28 | 28925 | 28925 | 1452 | 96.3 | 0.201 | 0.251 | 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] | |
6.28 | 0.43 | -7.2 | -6.77 | -0.38 | 0.49 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 22 |
c_scangle_it | 3.215 |
c_mcangle_it | 2.293 |
c_scbond_it | 2.174 |
c_mcbond_it | 1.421 |
c_angle_deg | 1.243 |
c_improper_angle_d | 0.98 |
c_bond_d | 0.007 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4123 |
Nucleic Acid Atoms | |
Solvent Atoms | 346 |
Heterogen Atoms | 36 |
Software
Software | |
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Software Name | Purpose |
SCALA | data scaling |
PHASER | phasing |
CNS | refinement |
PDB_EXTRACT | data extraction |
MAR345dtb | data collection |
xia2 | data reduction |
xia2 | data scaling |