4OF4 | pdb_00004of4

X-ray structure of unliganded uridine phosphorylase from Yersinia pseudotuberculosis at 1.4 A resolution

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4I2V

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.8	277	1M TRIS, 5% W/V PGA-LM, 20% W/V PEG 2000 MME, pH 7.8, VAPOR DIFFUSION, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
1.87	34.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 150.949	α = 90
b = 150.949	β = 90
c = 46.231	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	PIXEL	PSI PILATUS 6M		2013-12-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, DESY BEAMLINE P11	1.000	PETRA III, DESY	P11

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.4	75.475	99.8	0.059	14.7	4.9	76922	76922		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.4	1.48	99		0.626	0.626	0.319	1.2	4.8	11096

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4I2V	1.4	75.47	76922	76922	3859	99.88	0.1541	0.1541	0.1524	0.15	0.1838	0.18	RANDOM	18.103

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]
-0.16	-0.08		-0.16		0.24

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.655
r_dihedral_angle_4_deg	15.922
r_dihedral_angle_3_deg	12.915
r_dihedral_angle_1_deg	5.828
r_scangle_it	2.719
r_scbond_it	1.738
r_angle_refined_deg	1.165
r_mcangle_it	1.101
r_rigid_bond_restr	0.74
r_mcbond_it	0.633

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.655
r_dihedral_angle_4_deg	15.922
r_dihedral_angle_3_deg	12.915
r_dihedral_angle_1_deg	5.828
r_scangle_it	2.719
r_scbond_it	1.738
r_angle_refined_deg	1.165
r_mcangle_it	1.101
r_rigid_bond_restr	0.74
r_mcbond_it	0.633
r_chiral_restr	0.076
r_bond_refined_d	0.007
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3770
Nucleic Acid Atoms
Solvent Atoms	434
Heterogen Atoms	20

Software

Software
Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
DNA	data collection
XDS	data reduction

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 R01GM157729.