Experiment: 3OPX

Crystal structure of pyrimidine 5 -nucleotidase SDT1 from Saccharomyces cerevisiae complexed with uridine 5'-monophosphate

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3ONN	PDB ENTRY 3ONN

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	287	30% PEG4000, 0.1M Tris-HCl buffer, pH 8.5, 0.2M sodium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 287.0K

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.198	α = 90
b = 78.037	β = 90
c = 82.789	γ = 90

Symmetry
Space Group	P 21 21 21

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	RAYONIX MX-225		2010-03-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U	0.9194	SSRF	BL17U

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	1.7	35	99.9	0.051	39.6	7.3	30175	30137	2	2

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)
	1.7	1.73	100		0.347	5.4	7.2	1471

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	PDB ENTRY 3ONN	1.7	29.201	0.14	30113	29463	1493	97.84	0.2187	0.2141	0.2121	0.2123	0.2509	0.2482

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]
1.5032			-3.8577		2.3545

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	20.765
f_angle_d	1.092
f_chiral_restr	0.079
f_bond_d	0.007
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1967
Nucleic Acid Atoms
Solvent Atoms	167
Heterogen Atoms	15

Software

Software
Software Name	Purpose
MAR345dtb	data collection
MOLREP	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling