5C80

X-ray structure uridine phosphorylase from Vibrio cholerae in complex with uridine at 2.24 A resolution

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	293	PEG4000, 0.1M TRIS-HCl, 0.2M MgCl2x6H2O

Crystal Properties
Matthews coefficient	Solvent content
2.12	41.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.255	α = 71.81
b = 73.11	β = 77.19
c = 83.137	γ = 85.69

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	PIXEL	PSI PILATUS 6M		2015-05-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.97989	BESSY	14.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.243	77.231	91.1	0.055	0.077	0.055	9.6	1.7	58293	58293

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	2.243	2.36	83.2		0.333	0.333	0.333	2.3	1.7	7810

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4LWZ	2.243	45.47	55318	2849	90.88	0.1716	0.1683	0.237	RANDOM	30.999

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]
-0.05	-0.04	0.08	-0.17	0.01	0.18

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.205
r_dihedral_angle_4_deg	19.146
r_dihedral_angle_3_deg	15.511
r_dihedral_angle_1_deg	6.204
r_mcangle_it	2.539
r_scbond_it	1.872
r_mcbond_it	1.546
r_angle_refined_deg	1.532
r_chiral_restr	0.118
r_bond_refined_d	0.009

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.205
r_dihedral_angle_4_deg	19.146
r_dihedral_angle_3_deg	15.511
r_dihedral_angle_1_deg	6.204
r_mcangle_it	2.539
r_scbond_it	1.872
r_mcbond_it	1.546
r_angle_refined_deg	1.532
r_chiral_restr	0.118
r_bond_refined_d	0.009
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11263
Nucleic Acid Atoms
Solvent Atoms	822
Heterogen Atoms	167

Software

Software
Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

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.