5EFO | pdb_00005efo

X-ray structure uridine phosphorylase from Vibrio cholerae in complex with cytidine and cytosine at 1.63A.

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
2.24	45.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.949	α = 67.54
b = 76.336	β = 73.74
c = 89.694	γ = 84.92

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		2015-05-15	M	MAD

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	1.63	45.157	93.2	0.08	0.096	0.053	10.5	3.3	164109	164109

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	1.63	1.72	84.2		0.428	0.428	0.281	1.7	3.2	21679

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	4LWZ	1.63	19.97	154258	8011	92.16	0.1652	0.163	0.16	0.2073	0.2	RANDOM	20.75

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	-0.17	0.04	-0.07	-0.11	0.13

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	37.684
r_dihedral_angle_2_deg	29.252
r_sphericity_bonded	19.343
r_dihedral_angle_4_deg	18.176
r_dihedral_angle_3_deg	13.038
r_dihedral_angle_1_deg	5.427
r_mcangle_it	3.311
r_rigid_bond_restr	3.09
r_scbond_it	3.069
r_mcbond_it	2.515

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	37.684
r_dihedral_angle_2_deg	29.252
r_sphericity_bonded	19.343
r_dihedral_angle_4_deg	18.176
r_dihedral_angle_3_deg	13.038
r_dihedral_angle_1_deg	5.427
r_mcangle_it	3.311
r_rigid_bond_restr	3.09
r_scbond_it	3.069
r_mcbond_it	2.515
r_angle_refined_deg	1.191
r_chiral_restr	0.078
r_bond_refined_d	0.007
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11262
Nucleic Acid Atoms
Solvent Atoms	1518
Heterogen Atoms	78

Software

Software
Software Name	Purpose
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
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.