4FAT

Ligand-binding domain of GluA2 (flip) ionotropic glutamate receptor in complex with an allosteric modulator


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3O28PDB entry 3O28

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.129818% PEG 4000, 50mM Lithium Sulphate, 100mM Sodium Cacodylate, pH 4.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.2946.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.866α = 90
b = 88.143β = 90
c = 47.391γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2006-03-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.95375ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.425910.05211.43.353240484342219.6
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.41.4561.90.1624.12.13252

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 3O281.4254843445898249590.90.1880.170160.168080.20938RANDOM14.912
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]
-0.61-0.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.224
r_dihedral_angle_4_deg24.731
r_dihedral_angle_3_deg14.972
r_dihedral_angle_1_deg6.173
r_angle_other_deg2.901
r_angle_refined_deg2.291
r_chiral_restr0.154
r_bond_refined_d0.021
r_gen_planes_refined0.011
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.224
r_dihedral_angle_4_deg24.731
r_dihedral_angle_3_deg14.972
r_dihedral_angle_1_deg6.173
r_angle_other_deg2.901
r_angle_refined_deg2.291
r_chiral_restr0.154
r_bond_refined_d0.021
r_gen_planes_refined0.011
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2043
Nucleic Acid Atoms
Solvent Atoms389
Heterogen Atoms77

Software

Software
Software NamePurpose
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling