2OFW | pdb_00002ofw

Crystal structure of the APSK domain of human PAPSS1 complexed with 2 APS molecules

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1M7G	pdb id 1M7G

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		295	reservoir: 18-20% PEG 3350, 0.25 M calcium acetate protein solution: 5-8 mg/ml protein, 3 mM APS, 5 mM MgCl2, 50 mM Tris pH 7.5, 50 mM KCl, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.28	46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 181.19	α = 90
b = 69.03	β = 116.61
c = 150.61	γ = 90

Symmetry
Space Group	C 1 2 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		2004-03-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-BM	0.9594	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	2.05	10	83.6	0.095	0.082	12.4	3.7	121588	101698

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)
	2.05	2.1	92.8		0.301	0.24	4.36	2.5	7260

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	pdb id 1M7G	2.05	10	101066	10107	97.47	0.223	0.217	0.22	0.282	0.28	RANDOM	27.759

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]
0.62		-0.02	-0.65		0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.362
r_dihedral_angle_4_deg	18.209
r_dihedral_angle_3_deg	16.318
r_dihedral_angle_1_deg	5.807
r_scangle_it	2.403
r_angle_refined_deg	1.729
r_scbond_it	1.575
r_mcangle_it	1.021
r_mcbond_it	0.611
r_nbtor_refined	0.302

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.362
r_dihedral_angle_4_deg	18.209
r_dihedral_angle_3_deg	16.318
r_dihedral_angle_1_deg	5.807
r_scangle_it	2.403
r_angle_refined_deg	1.729
r_scbond_it	1.575
r_mcangle_it	1.021
r_mcbond_it	0.611
r_nbtor_refined	0.302
r_symmetry_hbond_refined	0.224
r_nbd_refined	0.204
r_metal_ion_refined	0.201
r_xyhbond_nbd_refined	0.19
r_symmetry_vdw_refined	0.145
r_chiral_restr	0.087
r_bond_refined_d	0.011
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12417
Nucleic Acid Atoms
Solvent Atoms	832
Heterogen Atoms	438

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.