3AP2 | pdb_00003ap2

Crystal structure of human tyrosylprotein sulfotransferase-2 complexed with PAP,C4 peptide, and phosphate ion

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	293.4	0.1M sodium malonate (pH 5.0), 10% polyethylene glycol 3350, 1M sodium/potassium phosphate, VAPOR DIFFUSION, SITTING DROP, temperature 293.4K

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 138.379	α = 90
b = 138.379	β = 90
c = 228.547	γ = 120

Symmetry
Space Group	H 3 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	CCD	ADSC QUANTUM 315			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	1.0000	SPring-8	BL41XU

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	50	96.3	0.126	0.126	13.8	5.2	31865	31865

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)
1	2.4	2.44	68.4		0.585	0.585	1.4	3.4	1109

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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	2.4	35.49	30245	30245	1615	96.22	0.2094	0.20722	0.2034	0.24866	0.243	RANDOM	37.833

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]
0.03	0.02		0.03		-0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.259
r_dihedral_angle_4_deg	19.875
r_dihedral_angle_3_deg	17.395
r_dihedral_angle_1_deg	5.979
r_scangle_it	3.259
r_scbond_it	2.016
r_angle_refined_deg	1.581
r_mcangle_it	1.282
r_mcbond_it	0.683
r_chiral_restr	0.103

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.259
r_dihedral_angle_4_deg	19.875
r_dihedral_angle_3_deg	17.395
r_dihedral_angle_1_deg	5.979
r_scangle_it	3.259
r_scbond_it	2.016
r_angle_refined_deg	1.581
r_mcangle_it	1.282
r_mcbond_it	0.683
r_chiral_restr	0.103
r_bond_refined_d	0.014
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4864
Nucleic Acid Atoms
Solvent Atoms	54
Heterogen Atoms	65

Software

Software
Software Name	Purpose
ADSC	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.