3T9U

CNQX bound to an oxidized double cysteine mutant (A452C/S652C) of the ligand binding domain of GluA2


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3DP6PDB ENTRY 3DP6

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.527714-15% PEG8000, 0.1 M sodium cacodylate, 0.1-0.15 M zinc acetate, 0.25 M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.6152.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 114.724α = 90
b = 165.243β = 90
c = 47.651γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102010-10-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCHESS BEAMLINE A10.977CHESSA1

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.975092.80.050.0547.6576.46025460254-3
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)RedundancyNumber Unique Reflections (All)
11.972980.1650.1659.844.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3DP61.9733.556778303992.070.1680.165310.21883RANDOM22.76
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]
0.01-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.654
r_dihedral_angle_4_deg16.975
r_dihedral_angle_3_deg15.202
r_dihedral_angle_1_deg6.07
r_scangle_it5.381
r_scbond_it3.366
r_mcangle_it2.047
r_angle_refined_deg1.867
r_mcbond_it1.187
r_angle_other_deg1.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.654
r_dihedral_angle_4_deg16.975
r_dihedral_angle_3_deg15.202
r_dihedral_angle_1_deg6.07
r_scangle_it5.381
r_scbond_it3.366
r_mcangle_it2.047
r_angle_refined_deg1.867
r_mcbond_it1.187
r_angle_other_deg1.12
r_mcbond_other0.377
r_chiral_restr0.161
r_bond_refined_d0.024
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6044
Nucleic Acid Atoms
Solvent Atoms908
Heterogen Atoms56

Software

Software
Software NamePurpose
HKL-3000data collection
PHENIXmodel building
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing