4IP0 | pdb_00004ip0

X-Ray Structure of the Complex Uridine Phosphorylase from Vibrio cholerae with Phosphate Ion at 1.29 A Resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.5	291	potassium phosphate, ammonium sulfate, sodium sulfate, pH 7.5, VAPOR DIFFUSION, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.671	α = 69.63
b = 71.062	β = 72.56
c = 87.908	γ = 85.73

Symmetry
Space Group	P 1

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		2012-05-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X13	0.81	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	1.294	78.794	95.5	0.069	14.2	3.8	327958	327958

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.29	1.36	94.3		0.266	0.266	2.3	2.7	47257

Refinement

Statistics
Diffraction ID	Structure Solution Method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	1.294	18.934	2	324967	16457	94.66	0.1731	0.1718	0.17	0.1997	0.2	Random	11.4658

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]
-1.1486	0.7442	-0.0405	1.4473	1.1961	-0.2988

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	12.224
f_angle_d	1.216
f_chiral_restr	0.074
f_bond_d	0.008
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11257
Nucleic Acid Atoms
Solvent Atoms	1998
Heterogen Atoms	86

Software

Software
Software Name	Purpose
SCALA	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
DNA	data collection
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.