2ZPT

Crystal structure of mouse sulfotransferase SULT1D1 complex with PAP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1AQUPDB ENTRY 1AQU

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.529316% PEG 10000, 10mM dithiothreitol, 100mM Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.0860.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 155.819α = 90
b = 67.6β = 105.63
c = 42.696γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU JUPITER 210mirrorsMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL38B10.75SPring-8BL38B1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.155094.30.0440.04422.33.414220314220312.4
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.151.1969.20.3560.3562.12.110387

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1AQU1.1520.56135033715394.190.148560.148560.147940.16018RANDOM12.432
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]
-0.010.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.929
r_dihedral_angle_4_deg19.037
r_dihedral_angle_3_deg12.979
r_dihedral_angle_1_deg5.189
r_sphericity_free2.864
r_sphericity_bonded2.445
r_scangle_it2.238
r_scbond_it1.638
r_angle_refined_deg1.225
r_mcangle_it1.181
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.929
r_dihedral_angle_4_deg19.037
r_dihedral_angle_3_deg12.979
r_dihedral_angle_1_deg5.189
r_sphericity_free2.864
r_sphericity_bonded2.445
r_scangle_it2.238
r_scbond_it1.638
r_angle_refined_deg1.225
r_mcangle_it1.181
r_rigid_bond_restr0.864
r_mcbond_it0.772
r_nbtor_refined0.313
r_symmetry_vdw_refined0.201
r_nbd_refined0.2
r_symmetry_hbond_refined0.122
r_xyhbond_nbd_refined0.094
r_chiral_restr0.082
r_bond_refined_d0.007
r_gen_planes_refined0.005
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2414
Nucleic Acid Atoms
Solvent Atoms458
Heterogen Atoms33

Software

Software
Software NamePurpose
REFMACrefinement
BBSdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing