1XHY

X-ray structure of the Y702F mutant of the GluR2 ligand-binding core (S1S2J) in complex with kainate at 1.85 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1FW0 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5280PEG1000, Li2SO4, cacodylate , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 280K
Crystal Properties
Matthews coefficientSolvent content
2.441.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.727α = 90
b = 60.3β = 90
c = 48.489γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDMARRESEARCH2003-11-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X110.8110EMBL/DESY, HAMBURGX11

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
11.8520.498.90.07316.13.52443324433-3-316
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)
11.851.88960.4323

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1FW01.8520.372506423243123697.670.153530.20656RANDOM16.048
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]
-0.010.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.868
r_scangle_it5.573
r_scbond_it3.299
r_mcangle_it1.984
r_angle_refined_deg1.747
r_mcbond_it1.065
r_angle_other_deg0.885
r_symmetry_vdw_other0.308
r_nbd_other0.259
r_nbd_refined0.221
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.868
r_scangle_it5.573
r_scbond_it3.299
r_mcangle_it1.984
r_angle_refined_deg1.747
r_mcbond_it1.065
r_angle_other_deg0.885
r_symmetry_vdw_other0.308
r_nbd_other0.259
r_nbd_refined0.221
r_symmetry_hbond_refined0.198
r_xyhbond_nbd_refined0.184
r_chiral_restr0.13
r_nbtor_other0.094
r_symmetry_vdw_refined0.052
r_bond_refined_d0.019
r_gen_planes_refined0.009
r_bond_other_d0.003
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2021
Nucleic Acid Atoms
Solvent Atoms359
Heterogen Atoms40

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing