1YCJ

Crystal structure of the kainate receptor GluR5 ligand-binding core in complex with (S)-glutamate


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4279PEG4000, phosphat-citrate buffer, lithiumsulphate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 279K
Crystal Properties
Matthews coefficientSolvent content
2.2445

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.714α = 90
b = 57.901β = 102.51
c = 88.75γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDMARRESEARCH2004-11-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X110.8128EMBL/DESY, HAMBURGX11

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.942599.70.0518.53.13748937372-3326.9
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.942.011000.3143.93721

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 REPLACEMENTTHROUGHOUT1FTJ1.9520.335600187599.460.202950.202950.199410.26885RANDOM29.497
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]
1.11-0.95-0.59-0.93
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.676
r_dihedral_angle_3_deg17.347
r_dihedral_angle_4_deg16.866
r_dihedral_angle_1_deg7.116
r_scangle_it4.314
r_scbond_it2.955
r_mcangle_it1.994
r_angle_refined_deg1.876
r_mcbond_it1.312
r_nbtor_refined0.308
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.676
r_dihedral_angle_3_deg17.347
r_dihedral_angle_4_deg16.866
r_dihedral_angle_1_deg7.116
r_scangle_it4.314
r_scbond_it2.955
r_mcangle_it1.994
r_angle_refined_deg1.876
r_mcbond_it1.312
r_nbtor_refined0.308
r_symmetry_vdw_refined0.255
r_nbd_refined0.214
r_xyhbond_nbd_refined0.196
r_symmetry_hbond_refined0.159
r_chiral_restr0.142
r_bond_refined_d0.021
r_gen_planes_refined0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4038
Nucleic Acid Atoms
Solvent Atoms398
Heterogen Atoms55

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing