2ZYT

Crystal structure of mouse cytosolic sulfotransferase mSULT1D1 complex with PAPS


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2ZPTPDB ENTRY 2ZPT

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
3.3763.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 160.156α = 90
b = 65.154β = 104.2
c = 46.824γ = 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 BL38B11.0000SPring-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
11.555081.40.0930.09314.23.25533555335
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)
11.551.6142.80.5270.5271.22.52890

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2ZPT1.5534.6752526278281.290.191930.190970.21RANDOM22.943
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]
-0.01-0.010.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.094
r_dihedral_angle_4_deg19.716
r_dihedral_angle_3_deg12.737
r_dihedral_angle_1_deg5.117
r_scangle_it2.275
r_scbond_it1.463
r_angle_refined_deg1.2
r_mcangle_it0.946
r_mcbond_it0.593
r_nbtor_refined0.308
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.094
r_dihedral_angle_4_deg19.716
r_dihedral_angle_3_deg12.737
r_dihedral_angle_1_deg5.117
r_scangle_it2.275
r_scbond_it1.463
r_angle_refined_deg1.2
r_mcangle_it0.946
r_mcbond_it0.593
r_nbtor_refined0.308
r_symmetry_vdw_refined0.204
r_nbd_refined0.192
r_symmetry_hbond_refined0.115
r_xyhbond_nbd_refined0.104
r_chiral_restr0.082
r_bond_refined_d0.008
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2440
Nucleic Acid Atoms
Solvent Atoms229
Heterogen Atoms43

Software

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