2V3U

Structure of the ligand-binding core of the ionotropic glutamate receptor-like GluRdelta2 in complex with D-serine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2V3TPDB ENTRY 2V3T

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5HANGING DROP VAPOR DIFFUSION. 20% PEG4000, 0.1 M CACODYLATE PH 6.5, 0.2 M SODIUM THIOCYANATE
Crystal Properties
Matthews coefficientSolvent content
240

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 36.801α = 66.88
b = 40.307β = 79.31
c = 44.393γ = 86.46
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2006-01-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.1BESSY14.1

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
11.734092.30.04123.823508623.59
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)
11.731.8270.10.262.13.3

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2V3T1.7440.1921250115495.30.20.1970.25RANDOM24.16
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]
-0.730.260.540.64-0.07-0.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.776
r_dihedral_angle_4_deg17.371
r_dihedral_angle_3_deg15.315
r_dihedral_angle_1_deg11.478
r_scangle_it3.785
r_scbond_it2.415
r_mcangle_it1.75
r_angle_refined_deg1.526
r_mcbond_it1.019
r_nbtor_refined0.312
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.776
r_dihedral_angle_4_deg17.371
r_dihedral_angle_3_deg15.315
r_dihedral_angle_1_deg11.478
r_scangle_it3.785
r_scbond_it2.415
r_mcangle_it1.75
r_angle_refined_deg1.526
r_mcbond_it1.019
r_nbtor_refined0.312
r_symmetry_vdw_refined0.221
r_nbd_refined0.214
r_xyhbond_nbd_refined0.136
r_symmetry_hbond_refined0.127
r_chiral_restr0.111
r_bond_refined_d0.016
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2022
Nucleic Acid Atoms
Solvent Atoms135
Heterogen Atoms15

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing