Experiment: 1Y1R

Crystal Structure of the Uridine Phosphorylase from Salmonella Typhimurium in Complex with Inhibitor and Phosphate Ion at 2.11A Resolution

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1SJ9	PDB entry 1SJ9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.2	295	PEG 4000, SODIUM-ACETATE TRIHYDRATE, 2,2'-Anhydrouridine, sodium phosphate , pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.88	α = 90
b = 124.07	β = 90
c = 134.4	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	MARRESEARCH	mirrors	2004-06-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MPG/DESY, HAMBURG BEAMLINE BW6	1.05	MPG/DESY, HAMBURG	BW6

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	2.11	28.75	97.4	0.121	10.2	3.09		86174			10.4

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	2.11	2.15	90.4		0.325	3.87	2.85	6430

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1SJ9	2.11	28.75	2	83853	4192	97.5	0.182	0.18	0.18	0.1797	0.219	0.2183	RANDOM	21.2

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]
2.74			0.6		-3.34

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	23.9
c_scangle_it	7.27
c_scbond_it	4.75
c_mcangle_it	3.94
c_mcbond_it	2.6
c_angle_deg	1.5
c_improper_angle_d	0.83
c_bond_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10937
Nucleic Acid Atoms
Solvent Atoms	641
Heterogen Atoms	47

Software

Software
Software Name	Purpose
CNS	refinement
MAR345	data collection
XDS	data scaling
MOLREP	phasing