4JP5 | pdb_00004jp5

X-ray structure of uridine phosphorylase from Yersinia pseudotuberculosis in unliganded state at 2.27 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	6.5	291	10mM Tris HCl, 0.1M Tris-maleate-NaOH,20% (w/v) PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.75	α = 90
b = 93.75	β = 90
c = 146.58	γ = 120

Symmetry
Space Group	P 32

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		2012-12-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON		0.8266

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.27	48.86	98.1	0.123	11.71		66646	65380		-3	43.597

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.27	2.45	91.4		0.928	1.052	1.5

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	3DPS	2.27	48.86	65379	65379	3197	98.04	0.1792	0.1792	0.1781	0.18	0.2021	0.2	RANDOM	35.5649

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]
-2.92			-2.92		5.84

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.053
r_dihedral_angle_3_deg	14.1
r_dihedral_angle_4_deg	12.962
r_dihedral_angle_1_deg	4.552
r_angle_refined_deg	0.904
r_scangle_it	0.381
r_mcangle_it	0.341
r_scbond_it	0.223
r_mcbond_it	0.19
r_chiral_restr	0.059

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.053
r_dihedral_angle_3_deg	14.1
r_dihedral_angle_4_deg	12.962
r_dihedral_angle_1_deg	4.552
r_angle_refined_deg	0.904
r_scangle_it	0.381
r_mcangle_it	0.341
r_scbond_it	0.223
r_mcbond_it	0.19
r_chiral_restr	0.059
r_bond_refined_d	0.005
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10788
Nucleic Acid Atoms
Solvent Atoms	463
Heterogen Atoms	29

Software

Software
Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MxCuBE	data collection
XDS	data reduction
MOLREP	phasing

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.