3ETS | pdb_00003ets

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3ELQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	1.8M lithium sulfate, 0.1M sodium cacodylate, pH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.75	67.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 181.83	α = 90
b = 181.83	β = 90
c = 100.66	γ = 120

Symmetry
Space Group	P 32 1 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	PSI PILATUS 6M		2008-04-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA		SLS	X06SA

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)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.4	48	99.7	0.143	0.134	8.8	7.6	102818	102818	1	2.994	51.21

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)	Redundancy	Number Unique Reflections (All)
	2.4	2.53	100		0.55	0.51	3.7	6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3ELQ	2.4	38.43	2	72370	72370	1197	99.7	0.175	0.175	0.18	0.216	0.22	RANDOM	41.17

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]
-1.58	-0.79		-1.58		2.38

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.151
r_dihedral_angle_3_deg	13.964
r_dihedral_angle_4_deg	13.816
r_scangle_it	7.078
r_dihedral_angle_1_deg	6.583
r_scbond_it	5.516
r_mcangle_it	3.508
r_mcbond_it	3.314
r_mcbond_other	1.769
r_angle_refined_deg	1.376
r_angle_other_deg	0.982
r_symmetry_vdw_other	0.239
r_nbd_refined	0.235
r_nbd_other	0.232
r_symmetry_vdw_refined	0.229
r_nbtor_refined	0.189
r_xyhbond_nbd_refined	0.139
r_symmetry_hbond_refined	0.12
r_chiral_restr	0.088
r_nbtor_other	0.087
r_bond_refined_d	0.017
r_bond_other_d	0.007
r_gen_planes_refined	0.007
r_gen_planes_other	0.006
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 Atoms	Number
Protein Atoms	8915
Nucleic Acid Atoms
Solvent Atoms	181
Heterogen Atoms	56

Software

Software
Software Name	Purpose
RemDAq	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
SCALA	data scaling