5WRJ

Crystal structure of human tyrosylprotein sulfotransferase-1 complexed with PAP and gastrin peptide


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.2 M potassium sodium tartrate trihydrate, 19.5% w/v polyethylene glycol 3350
Crystal Properties
Matthews coefficientSolvent content
2.9958.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.668α = 90.6
b = 93.263β = 93.39
c = 93.012γ = 103.39
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-2252015-10-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL38B11.000SPring-8BL38B1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.335097.50.1558.331.971093

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 REPLACEMENTTHROUGHOUT5WRI2.3148.9967464356095.920.24240.240960.26943RANDOM46.267
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]
0.01-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.406
r_dihedral_angle_3_deg13.746
r_dihedral_angle_4_deg11.896
r_dihedral_angle_1_deg5.055
r_long_range_B_refined3.612
r_long_range_B_other3.594
r_angle_other_deg3.563
r_scangle_other2.05
r_mcangle_it1.955
r_mcangle_other1.955
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.406
r_dihedral_angle_3_deg13.746
r_dihedral_angle_4_deg11.896
r_dihedral_angle_1_deg5.055
r_long_range_B_refined3.612
r_long_range_B_other3.594
r_angle_other_deg3.563
r_scangle_other2.05
r_mcangle_it1.955
r_mcangle_other1.955
r_scbond_it1.194
r_scbond_other1.194
r_angle_refined_deg1.175
r_mcbond_it1.162
r_mcbond_other1.162
r_chiral_restr0.062
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_gen_planes_other0.003
r_bond_other_d
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 Atoms8872
Nucleic Acid Atoms108
Solvent Atoms144
Heterogen Atoms40

Software

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