4U90

GephE in complex with PEG crosslinked GABA receptor alpha3 subunit derived dimeric peptide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2FU3 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.52770.1 M sodium acetate pH 4.5, 20-30 % 2-Methyl-2,4-pentanediol.
Crystal Properties
Matthews coefficientSolvent content
2.6253.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.538α = 90
b = 99.24β = 90
c = 114.406γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2014-05-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.9100ESRFID23-1

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
1244.2990.06514.15.534354
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)
122.051000.6232.25.7

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 REPLACEMENTTHROUGHOUT2FU322032616169499.670.168780.166550.21103RANDOM53.214
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]
-0.13-1.51.63
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.854
r_dihedral_angle_4_deg21.521
r_dihedral_angle_3_deg16.241
r_long_range_B_refined8.999
r_long_range_B_other8.999
r_dihedral_angle_1_deg6.63
r_scangle_other6.199
r_mcangle_it4.44
r_mcangle_other4.44
r_scbond_it4.296
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.854
r_dihedral_angle_4_deg21.521
r_dihedral_angle_3_deg16.241
r_long_range_B_refined8.999
r_long_range_B_other8.999
r_dihedral_angle_1_deg6.63
r_scangle_other6.199
r_mcangle_it4.44
r_mcangle_other4.44
r_scbond_it4.296
r_scbond_other4.286
r_mcbond_it3.173
r_mcbond_other3.172
r_angle_refined_deg1.907
r_angle_other_deg0.933
r_chiral_restr0.111
r_bond_refined_d0.019
r_gen_planes_refined0.009
r_bond_other_d0.002
r_gen_planes_other0.001
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3293
Nucleic Acid Atoms
Solvent Atoms255
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing