4F22

Kainate bound to the K660A mutant of the ligand binding domain of GluA3


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3DLN 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.527714-15% PEG 8K, 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
2.7655.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.657α = 90
b = 49.028β = 90
c = 136.639γ = 90
Symmetry
Space GroupP 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102010-12-05MSINGLE 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
12.065099.70.1570.15711.1125.1-3
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)
12.082.121000.3120.3122.2614.5

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 REPLACEMENTTHROUGHOUT3DLN2.0633.151113719058103398.40.1890.18450.181290.24362RANDOM22.342
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]
0.04-0.060.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.58
r_dihedral_angle_4_deg23.983
r_dihedral_angle_3_deg16.118
r_dihedral_angle_1_deg6.315
r_scangle_it5.112
r_scbond_it3.099
r_mcangle_it2.09
r_angle_refined_deg1.897
r_mcbond_it1.171
r_angle_other_deg1.006
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.58
r_dihedral_angle_4_deg23.983
r_dihedral_angle_3_deg16.118
r_dihedral_angle_1_deg6.315
r_scangle_it5.112
r_scbond_it3.099
r_mcangle_it2.09
r_angle_refined_deg1.897
r_mcbond_it1.171
r_angle_other_deg1.006
r_mcbond_other0.305
r_chiral_restr0.113
r_bond_refined_d0.022
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 Atoms2028
Nucleic Acid Atoms
Solvent Atoms235
Heterogen Atoms16

Software

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