2ZYW

crystal structure of mouse cytosolic sulfotransferase mSULT1D1 complex with PAP and p-nitrophenol, obtained by two-step soaking method


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 DTT, 100mM Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.160.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 155.313α = 90
b = 67.838β = 105.25
c = 42.867γ = 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
11.85099.70.0440.04423.93.63974339743
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)
11.81.8699.30.3870.3872.13.43966

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 2ZPT1.826.1537750199099.650.182820.182190.19451RANDOM24.162
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]
-0.010.05-0.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.893
r_dihedral_angle_4_deg18.602
r_dihedral_angle_3_deg12.811
r_dihedral_angle_1_deg5.138
r_scangle_it2.093
r_scbond_it1.344
r_angle_refined_deg1.128
r_mcangle_it0.905
r_mcbond_it0.545
r_nbtor_refined0.308
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.893
r_dihedral_angle_4_deg18.602
r_dihedral_angle_3_deg12.811
r_dihedral_angle_1_deg5.138
r_scangle_it2.093
r_scbond_it1.344
r_angle_refined_deg1.128
r_mcangle_it0.905
r_mcbond_it0.545
r_nbtor_refined0.308
r_symmetry_vdw_refined0.228
r_nbd_refined0.19
r_xyhbond_nbd_refined0.098
r_symmetry_hbond_refined0.097
r_chiral_restr0.079
r_bond_refined_d0.007
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2423
Nucleic Acid Atoms
Solvent Atoms226
Heterogen Atoms65

Software

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