5NS9

Crystal structure of the GluA2 LBD (L483Y-N754S-L758V) in complex with glutamate


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7277.1520% w/v PEG3350, 200mM Li2SO4
Crystal Properties
Matthews coefficientSolvent content
2.2344.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.99α = 90
b = 121.297β = 90
c = 47.083γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6Mmirror2014-11-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.918BESSY14.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.444899.211.654.2799346

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 REPLACEMENTFREE R-VALUE1FTJ1.4447.9994378496899.190.15010.147220.20486RANDOM19.624
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]
0.030.72-0.75
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free34.226
r_dihedral_angle_2_deg30.783
r_dihedral_angle_4_deg15.445
r_sphericity_bonded13.808
r_dihedral_angle_3_deg11.812
r_dihedral_angle_1_deg6.045
r_long_range_B_refined4.891
r_rigid_bond_restr4.05
r_long_range_B_other3.834
r_scangle_other3.463
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free34.226
r_dihedral_angle_2_deg30.783
r_dihedral_angle_4_deg15.445
r_sphericity_bonded13.808
r_dihedral_angle_3_deg11.812
r_dihedral_angle_1_deg6.045
r_long_range_B_refined4.891
r_rigid_bond_restr4.05
r_long_range_B_other3.834
r_scangle_other3.463
r_scbond_it3.457
r_scbond_other3.288
r_mcangle_it2.508
r_mcangle_other2.508
r_mcbond_it2.168
r_mcbond_other2.168
r_angle_refined_deg2.062
r_angle_other_deg1.109
r_chiral_restr0.165
r_bond_refined_d0.025
r_gen_planes_refined0.012
r_bond_other_d0.002
r_gen_planes_other0.002
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_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4083
Nucleic Acid Atoms
Solvent Atoms905
Heterogen Atoms87

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing