3PMV

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 3O28 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP427718% PEG 4000, 50mM Lithium Sulphate, 2.5% Glycerol, 100mM Sodium Cacodylate pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.2745.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.22α = 90
b = 87.23β = 90
c = 47.4γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++Mirrors2007-03-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.54178

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
11.7943.6198.10.0513.24.12489124891226.1
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)
1.81.8682.90.2873.52.92050

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 REPLACEMENTTHROUGHOUT3O281.843.612363123631125998.10.19870.187160.183940.25232RANDOM18.709
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]
-0.331.04-0.71
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.004
r_dihedral_angle_4_deg18.652
r_dihedral_angle_3_deg14.404
r_dihedral_angle_1_deg5.919
r_scangle_it4.305
r_scbond_it3.213
r_mcangle_it1.953
r_mcbond_it1.724
r_angle_refined_deg1.613
r_angle_other_deg1.357
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.004
r_dihedral_angle_4_deg18.652
r_dihedral_angle_3_deg14.404
r_dihedral_angle_1_deg5.919
r_scangle_it4.305
r_scbond_it3.213
r_mcangle_it1.953
r_mcbond_it1.724
r_angle_refined_deg1.613
r_angle_other_deg1.357
r_mcbond_other0.395
r_symmetry_hbond_refined0.273
r_symmetry_vdw_refined0.251
r_symmetry_vdw_other0.232
r_nbd_refined0.205
r_nbd_other0.197
r_xyhbond_nbd_refined0.193
r_nbtor_refined0.174
r_chiral_restr0.097
r_nbtor_other0.089
r_bond_refined_d0.017
r_gen_planes_refined0.007
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2043
Nucleic Acid Atoms
Solvent Atoms359
Heterogen Atoms86

Software

Software
Software NamePurpose
CrystalCleardata collection
AMoREphasing
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling