3QFK

2.05 Angstrom Crystal Structure of Putative 5'-Nucleotidase from Staphylococcus aureus in complex with alpha-ketoglutarate

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	295	Protein: 7.1 mg/mL, 0.25M Sodium chloride, Tris-HCl pH 8.3, Screen: PEGs II (C11), 0.2M Lithium sulfate, 0.1M Tris pH 8.5, 20% PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.444	α = 90
b = 84.689	β = 116.91
c = 95.966	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 300 mm CCD	Beryllium lenses	2010-10-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	30	98.8	0.066	13.4	3.7	40617	40617		-3	41.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.05	2.09	88.9		0.489	2.05	2.9	1827

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.05	29.2	36636	36636	1928	95.05	0.17557	0.17557	0.17323	0.22146	RANDOM	49.413

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]
-2.51		-2.53	2.37		-2.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.013
r_dihedral_angle_3_deg	9.207
r_dihedral_angle_4_deg	7.853
r_scangle_it	4.594
r_scbond_it	3.09
r_dihedral_angle_1_deg	2.95
r_mcangle_it	1.9
r_angle_refined_deg	1.426
r_mcbond_it	1.101
r_angle_other_deg	0.818

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.013
r_dihedral_angle_3_deg	9.207
r_dihedral_angle_4_deg	7.853
r_scangle_it	4.594
r_scbond_it	3.09
r_dihedral_angle_1_deg	2.95
r_mcangle_it	1.9
r_angle_refined_deg	1.426
r_mcbond_it	1.101
r_angle_other_deg	0.818
r_mcbond_other	0.313
r_chiral_restr	0.082
r_bond_refined_d	0.012
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4092
Nucleic Acid Atoms
Solvent Atoms	227
Heterogen Atoms	23

Software

Software
Software Name	Purpose
Blu-Ice	data collection
PHENIX	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.