4NY1

X-ray structure of the unliganded uridine phosphorylase from Yersinia pseudotuberculosis at 1.7 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.8	277	1M Tris, 5% w/v PGA-LM, 20% w/v PEG 2000 MME, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
1.87	34.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 150.742	α = 90
b = 150.742	β = 90
c = 46.31	γ = 120

Symmetry
Space Group	H 3

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	Bruker Platinum 135		2013-11-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR	1.5419

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	1.7	75.4	97.6	0.0578	0.0871	9.29	1.89	42114	42114			21.6

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	1.7	1.73	94.5		0.3353	1.64	1.52	2202

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	MOLECULAR REPLACEMENT	THROUGHOUT	1.7	37.686	43172	42114	2124	97.55	0.1631	0.1631	0.1615	0.1938	RANDOM	12.5657

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]
-0.09	-0.04		-0.09		0.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.182
r_dihedral_angle_4_deg	16.253
r_dihedral_angle_3_deg	12.376
r_dihedral_angle_1_deg	5.496
r_scangle_it	2.042
r_scbond_it	1.159
r_angle_refined_deg	1.01
r_mcangle_it	0.996
r_mcbond_it	0.537
r_rigid_bond_restr	0.53

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.182
r_dihedral_angle_4_deg	16.253
r_dihedral_angle_3_deg	12.376
r_dihedral_angle_1_deg	5.496
r_scangle_it	2.042
r_scbond_it	1.159
r_angle_refined_deg	1.01
r_mcangle_it	0.996
r_mcbond_it	0.537
r_rigid_bond_restr	0.53
r_chiral_restr	0.069
r_bond_refined_d	0.006
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3758
Nucleic Acid Atoms
Solvent Atoms	482
Heterogen Atoms	24

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
PROTEUM PLUS	data collection
PROTEUM PLUS	data reduction
SCALEPACK	data scaling
PHASER	phasing

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 R01GM133198.