3FWP | pdb_00003fwp

X-ray structure of uridine nucleoside phosphorylease from Salmonella typhimurium complexed with phosphate and its inhibitor 2,2'-anhydrouridine at 1.86 A resolution

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.2	295	PEG400, NaN3, GLYCEROL, PEG3350. K2HPO4, ANU, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.79	α = 90
b = 124.07	β = 90
c = 134.1	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	MAR CCD 165 mm		2004-12-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X13	0.85	EMBL/DESY, HAMBURG	X13

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	1.86	88	88.4	0.094			124633	110180		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.86	1.87	93.6		0.506	2.49		1963

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	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	3DPS	1.86	27.99	104669	5509	88.44	0.17765	0.17615	0.18	0.20617	0.21	RANDOM	20.376

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]
0.8			-0.3		-0.5

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.064
r_dihedral_angle_4_deg	15.724
r_dihedral_angle_3_deg	12.966
r_dihedral_angle_1_deg	5.596
r_scangle_it	1.922
r_scbond_it	1.072
r_angle_refined_deg	1.066
r_mcangle_it	0.819
r_mcbond_it	0.436
r_nbtor_refined	0.294

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.064
r_dihedral_angle_4_deg	15.724
r_dihedral_angle_3_deg	12.966
r_dihedral_angle_1_deg	5.596
r_scangle_it	1.922
r_scbond_it	1.072
r_angle_refined_deg	1.066
r_mcangle_it	0.819
r_mcbond_it	0.436
r_nbtor_refined	0.294
r_nbd_refined	0.19
r_symmetry_vdw_refined	0.145
r_symmetry_hbond_refined	0.112
r_xyhbond_nbd_refined	0.109
r_metal_ion_refined	0.099
r_chiral_restr	0.069
r_bond_refined_d	0.007
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10965
Nucleic Acid Atoms
Solvent Atoms	1015
Heterogen Atoms	66

Software

Software
Software Name	Purpose
DENZO	data reduction
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

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.