5OBH

Crystal structure of glycine binding protein in complex with bicuculline


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5OAN 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5293Reservoir buffer: 0.2 M ammonium formate, 20 % PEG 3350 Protein buffer: 50 mM tris, 250 mM NaCl, pH 7.5. 2 mM bicuculline
Crystal Properties
Matthews coefficientSolvent content
2.2144.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.243α = 90
b = 132.236β = 90
c = 132.631γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray150CCDRIGAKU SATURN 944+2016-11-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.54157

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
12.446.821000.130.9957.96.24981748.1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.481000.7760.8261.86.2

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 REPLACEMENTTHROUGHOUT5oan2.446.8247302244799.930.230540.229550.24944RANDOM45.177
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]
1.120.27-1.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.703
r_dihedral_angle_4_deg21.411
r_dihedral_angle_3_deg13.774
r_long_range_B_refined7.746
r_long_range_B_other7.739
r_dihedral_angle_1_deg6.646
r_scangle_other4.637
r_mcangle_it4.634
r_mcangle_other4.629
r_scbond_it2.773
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.703
r_dihedral_angle_4_deg21.411
r_dihedral_angle_3_deg13.774
r_long_range_B_refined7.746
r_long_range_B_other7.739
r_dihedral_angle_1_deg6.646
r_scangle_other4.637
r_mcangle_it4.634
r_mcangle_other4.629
r_scbond_it2.773
r_scbond_other2.773
r_mcbond_it2.755
r_mcbond_other2.755
r_angle_refined_deg1.418
r_angle_other_deg0.919
r_chiral_restr0.08
r_bond_refined_d0.009
r_bond_other_d0.006
r_gen_planes_refined0.005
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 Atoms8192
Nucleic Acid Atoms
Solvent Atoms404
Heterogen Atoms215

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing