2F34

Crystal Structure of the GluR5 Ligand Binding Core Dimer with UBP310 At 1.74 Angstroms Resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.629317-22% PEG 1K 100mM TRIS 5mM UBP310, pH 8.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.6453.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 97.698α = 90
b = 97.954β = 90
c = 129.126γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2005-08-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.00000APS22-ID

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
11.744099.90.03814.54.964151641511125.16
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)
11.741.899.70.4413.384.9

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1TXF1.7433.416037860378321899.920.182550.182550.181030.21135RANDOM19.284
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]
0.260.21-0.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.879
r_dihedral_angle_4_deg13.203
r_dihedral_angle_3_deg10.626
r_dihedral_angle_1_deg2.762
r_scangle_it1.876
r_mcangle_it1.718
r_angle_refined_deg1.661
r_scbond_it1.33
r_mcbond_it1.123
r_nbtor_refined0.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.879
r_dihedral_angle_4_deg13.203
r_dihedral_angle_3_deg10.626
r_dihedral_angle_1_deg2.762
r_scangle_it1.876
r_mcangle_it1.718
r_angle_refined_deg1.661
r_scbond_it1.33
r_mcbond_it1.123
r_nbtor_refined0.32
r_symmetry_vdw_refined0.276
r_nbd_refined0.262
r_xyhbond_nbd_refined0.228
r_symmetry_hbond_refined0.227
r_chiral_restr0.124
r_bond_refined_d0.014
r_gen_planes_refined0.007
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 Atoms4014
Nucleic Acid Atoms
Solvent Atoms482
Heterogen Atoms82

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing