2ZYU

Crystal structure of mouse cytosolic sulfotransferase mSULT1D1 complex with PAPS and p-nitrophenyl sulfate


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
2.9658.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 152.867α = 90
b = 66.573β = 106.1
c = 42.557γ = 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
11.75095.70.0430.04327.52.94421044210
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)
11.71.7693.70.8170.8171.12.54301

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 2ZPT1.824.6634757186596.150.194950.193380.22359RANDOM27.366
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.832
r_dihedral_angle_4_deg19.647
r_dihedral_angle_3_deg13.676
r_dihedral_angle_1_deg5.599
r_scangle_it2.984
r_scbond_it1.896
r_angle_refined_deg1.421
r_mcangle_it1.302
r_mcbond_it0.828
r_nbtor_refined0.328
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.832
r_dihedral_angle_4_deg19.647
r_dihedral_angle_3_deg13.676
r_dihedral_angle_1_deg5.599
r_scangle_it2.984
r_scbond_it1.896
r_angle_refined_deg1.421
r_mcangle_it1.302
r_mcbond_it0.828
r_nbtor_refined0.328
r_symmetry_vdw_refined0.26
r_nbd_refined0.208
r_symmetry_hbond_refined0.165
r_xyhbond_nbd_refined0.148
r_chiral_restr0.087
r_bond_refined_d0.011
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2423
Nucleic Acid Atoms
Solvent Atoms173
Heterogen Atoms57

Software

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