5OBG

Crystal structure of glycine binding protein in complex with strychnine


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: 20 % PEG 3350, 0.2 M MgOAc Protein buffer: 50 mM tris, 250 mM NaCl, pH 7.5, 0.5 mM strychnine
Crystal Properties
Matthews coefficientSolvent content
2.6152.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.353α = 90
b = 100.04β = 90
c = 163.752γ = 90
Symmetry
Space GroupP 2 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray150CCDRIGAKU SATURN 944+2017-04-11MSINGLE 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
1247.921000.1470.9926.16.210084319
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)
122.031000.5890.6571.96.2

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 REPLACEMENTTHROUGHOUT5oan247.9295620515799.990.199280.196580.24961RANDOM27.39
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]
-0.21-0.180.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.831
r_dihedral_angle_4_deg19.93
r_dihedral_angle_3_deg14.109
r_dihedral_angle_1_deg7.342
r_long_range_B_refined6.763
r_long_range_B_other6.763
r_scangle_other4.758
r_mcangle_it3.435
r_mcangle_other3.435
r_scbond_it3.084
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.831
r_dihedral_angle_4_deg19.93
r_dihedral_angle_3_deg14.109
r_dihedral_angle_1_deg7.342
r_long_range_B_refined6.763
r_long_range_B_other6.763
r_scangle_other4.758
r_mcangle_it3.435
r_mcangle_other3.435
r_scbond_it3.084
r_scbond_other3.084
r_mcbond_it2.31
r_mcbond_other2.306
r_angle_refined_deg1.95
r_angle_other_deg1.094
r_chiral_restr0.107
r_bond_refined_d0.018
r_gen_planes_refined0.009
r_bond_other_d0.008
r_gen_planes_other0.002
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 Atoms8305
Nucleic Acid Atoms
Solvent Atoms749
Heterogen Atoms346

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing