3ETT

Crystal structure of a bacterial arylsulfate sulfotransferase catalytic intermediate with 4-nitrophenol bound in the active site


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3ELQ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52931.8M lithium sulfate, 0.1M sodium cacodylate, pH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.7567.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 181.503α = 90
b = 181.503β = 90
c = 99.984γ = 120
Symmetry
Space GroupP 32 1 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2008-04-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SASLSX06SA

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
12.15099.60.0940.0818.13.810876810876812.99430.47
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)
2.12.2199.60.540.462.43.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)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 REPLACEMENTTHROUGHOUT3ELQ2.133.982106194106194176999.60.1880.1880.1870.232RANDOM29.37
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]
-2.76-1.38-2.764.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.191
r_dihedral_angle_4_deg14.993
r_dihedral_angle_3_deg13.537
r_dihedral_angle_1_deg6.951
r_scangle_it4.312
r_scbond_it3.445
r_mcangle_it2.087
r_mcbond_it1.93
r_angle_refined_deg1.647
r_angle_other_deg1.164
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.191
r_dihedral_angle_4_deg14.993
r_dihedral_angle_3_deg13.537
r_dihedral_angle_1_deg6.951
r_scangle_it4.312
r_scbond_it3.445
r_mcangle_it2.087
r_mcbond_it1.93
r_angle_refined_deg1.647
r_angle_other_deg1.164
r_mcbond_other1.005
r_symmetry_vdw_refined0.248
r_nbd_refined0.23
r_symmetry_vdw_other0.228
r_nbd_other0.223
r_nbtor_refined0.186
r_symmetry_hbond_refined0.166
r_xyhbond_nbd_refined0.147
r_chiral_restr0.104
r_nbtor_other0.089
r_bond_refined_d0.021
r_bond_other_d0.015
r_gen_planes_refined0.008
r_gen_planes_other0.006
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8919
Nucleic Acid Atoms
Solvent Atoms754
Heterogen Atoms50

Software

Software
Software NamePurpose
RemDAqdata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling