2QS1

Crystal structure of the GluR5 ligand binding core dimer in complex with UBP315 at 1.80 Angstroms resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2F34pdb entry 2F34

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.929318% PEG 1K, 100 mM Tris-Cl, 2.5 mM UBP315, pH 8.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.6453.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 97.823α = 90
b = 97.816β = 90
c = 129.043γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2006-12-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEOTHER1.5418

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
11.84099.90.0420.93.557347573471127.42
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)
11.81.8699.80.2734.733.4

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTpdb entry 2F341.821.575446354463288499.910.198640.198640.197560.21916RANDOM34.393
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.37
r_dihedral_angle_4_deg13.754
r_dihedral_angle_3_deg13.738
r_dihedral_angle_1_deg5.261
r_scangle_it1.9
r_angle_refined_deg1.331
r_scbond_it1.294
r_mcangle_it0.867
r_mcbond_it0.523
r_nbtor_refined0.297
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.37
r_dihedral_angle_4_deg13.754
r_dihedral_angle_3_deg13.738
r_dihedral_angle_1_deg5.261
r_scangle_it1.9
r_angle_refined_deg1.331
r_scbond_it1.294
r_mcangle_it0.867
r_mcbond_it0.523
r_nbtor_refined0.297
r_symmetry_vdw_refined0.203
r_nbd_refined0.186
r_xyhbond_nbd_refined0.146
r_symmetry_hbond_refined0.087
r_chiral_restr0.079
r_bond_refined_d0.008
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4014
Nucleic Acid Atoms
Solvent Atoms366
Heterogen Atoms86

Software

Software
Software NamePurpose
REFMACrefinement
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling