5IJJ

Structure of the SPX domain of Chaetomium thermophilum Glycerophosphodiester Phosphodiesterase 1 in complex with inositol hexakisphosphate (InsP6)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529825% PEG 3350, 0.1M ammonium acetate, 0.1M BisTris
Crystal Properties
Matthews coefficientSolvent content
2.3146.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.363α = 90
b = 53.366β = 113.42
c = 94.314γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2015-05-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA1.000000SLSX06DA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.9550970.06120.56.728959-341
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.952.0782.82.286.5

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 REPLACEMENTTHROUGHOUT5IIG1.9519.5927510144897.120.204210.201730.25089RANDOM46.756
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]
3.650.8-1.6-2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.548
r_dihedral_angle_4_deg21.004
r_dihedral_angle_3_deg15.448
r_long_range_B_refined9.195
r_long_range_B_other9.19
r_dihedral_angle_1_deg5.683
r_scangle_other4.735
r_scbond_it3.169
r_scbond_other3.168
r_angle_refined_deg2.229
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.548
r_dihedral_angle_4_deg21.004
r_dihedral_angle_3_deg15.448
r_long_range_B_refined9.195
r_long_range_B_other9.19
r_dihedral_angle_1_deg5.683
r_scangle_other4.735
r_scbond_it3.169
r_scbond_other3.168
r_angle_refined_deg2.229
r_mcangle_it2.195
r_mcangle_other2.195
r_mcbond_it1.511
r_mcbond_other1.51
r_angle_other_deg1.096
r_chiral_restr0.133
r_bond_refined_d0.022
r_gen_planes_refined0.011
r_bond_other_d0.002
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 Atoms2678
Nucleic Acid Atoms
Solvent Atoms84
Heterogen Atoms128

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing