2BDU

X-Ray Structure of a Cytosolic 5'-Nucleotidase III from Mus Musculus MM.158936

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	277	10 MG/ML PROTEIN, 26% PEG 8K, 0.10 M MOPS (HEPES USED AS CRYOPROTECTANT), pH 7.0, vapor diffusion, hanging drop, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3	58.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 133.674	α = 90
b = 133.674	β = 90
c = 38.889	γ = 120

Symmetry
Space Group	P 32

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	HORIZONTAL SAGITALLY FOCUSING 2ND BENT MONOCHROMATOR CRYSTAL, VERTICAL BENT FOCUSING MIRROR	2005-10-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	0.97911	APS	22-ID

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	2.35	43.755	98.5	0.091	6.818	5.4		31917

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)
1	2.35	2.4	87.8	87.8	0.367	2.067	3.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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	2.35	43.755	31910	1619	98.503	0.1659	0.16588	0.163	0.2198	RANDOM	48.154

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]
0.303	0.151		0.303		-0.454

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.957
r_dihedral_angle_4_deg	23.413
r_dihedral_angle_3_deg	16.224
r_dihedral_angle_1_deg	6.439
r_scangle_it	6.275
r_scbond_it	4.645
r_mcangle_it	2.414
r_angle_refined_deg	1.548
r_mcbond_it	1.379
r_nbtor_refined	0.303

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.957
r_dihedral_angle_4_deg	23.413
r_dihedral_angle_3_deg	16.224
r_dihedral_angle_1_deg	6.439
r_scangle_it	6.275
r_scbond_it	4.645
r_mcangle_it	2.414
r_angle_refined_deg	1.548
r_mcbond_it	1.379
r_nbtor_refined	0.303
r_symmetry_vdw_refined	0.223
r_nbd_refined	0.207
r_xyhbond_nbd_refined	0.169
r_symmetry_hbond_refined	0.134
r_chiral_restr	0.107
r_bond_refined_d	0.019
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4652
Nucleic Acid Atoms
Solvent Atoms	359
Heterogen Atoms	30

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHARP	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
PHENIX	phasing
SHELXD	phasing
SOLOMON	phasing
ARP/wARP	model building

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.