2OFX | pdb_00002ofx

crystal structure of the APSK domain of human PAPSS1 in complex with ADPMg and PAPS

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2OFW

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.3	298	reservoir: 0.2-0.4mM ammonium dihydrogenphosphate protein solution: 6 mg/ml protein, 2 mM PAPS, 2 mM ADP, 5 mM MgCl2, 50 mM Tris pH 7.5, 50 mM KCl , pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
1.99	38.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.4	α = 90
b = 63.32	β = 114.38
c = 61.69	γ = 90

Symmetry
Space Group	P 1 21 1

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	MARMOSAIC 225 mm CCD		2004-12-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-BM	1.0	APS	22-BM

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	1.89	20	97.5	0.079	0.071	18.83	5.6	28560	27832

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)
	1.89	2.01	94.5		0.165	0.148	9.3	5.13	4298

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	2OFW	1.9	20	27683	2766	97.14	0.192	0.187	0.19	0.236	0.23	RANDOM	13.1

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]
-0.22		0.11	1.16		-0.86

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.381
r_dihedral_angle_4_deg	15.15
r_dihedral_angle_3_deg	14.637
r_dihedral_angle_1_deg	6.03
r_scangle_it	2.967
r_scbond_it	2.021
r_angle_refined_deg	1.571
r_mcangle_it	1.26
r_mcbond_it	0.773
r_nbtor_refined	0.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.381
r_dihedral_angle_4_deg	15.15
r_dihedral_angle_3_deg	14.637
r_dihedral_angle_1_deg	6.03
r_scangle_it	2.967
r_scbond_it	2.021
r_angle_refined_deg	1.571
r_mcangle_it	1.26
r_mcbond_it	0.773
r_nbtor_refined	0.31
r_symmetry_hbond_refined	0.252
r_symmetry_vdw_refined	0.236
r_nbd_refined	0.21
r_xyhbond_nbd_refined	0.178
r_chiral_restr	0.092
r_metal_ion_refined	0.045
r_bond_refined_d	0.012
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3173
Nucleic Acid Atoms
Solvent Atoms	197
Heterogen Atoms	176

Software

Software
Software Name	Purpose
XSCALE	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

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.