4R2X | pdb_00004r2x

Unique conformation of uridine and asymmetry of the hexameric molecule revealed in the high-resolution structures of Shewanella oneidensis uridine phosphorylase in the free form and in complex with uridine

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1RXY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5.5	293	0.75M ammonium sulfate, 0.1M Bis-Tris, pH 5.5, 0.75% (w/v) PEG 3350, 25% (v/v) glycerol, temperature 293K, FREE INTERFACE DIFFUSION, temperature 293.0K

Crystal Properties
Matthews coefficient	Solvent content
2.16	43.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.54	α = 90
b = 95.93	β = 120
c = 91.61	γ = 90

Symmetry
Space Group	P 1 21 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	ADSC QUANTUM 315		2011-05-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL24XU		SPring-8	BL24XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	0.93	79.35	93.5	0.126	0.87	12.2	5.3		883288		1

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	0.95	1	93.4		0.661	0.708	2.6	4.8

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	1RXY	0.93	29.66	834827	43368	95.9	0.15	0.149	0.16	0.164	0.17	RANDOM	8.86

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]
-2.6		1.68	10.97		-8.36

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.628
r_sphericity_free	20.238
r_dihedral_angle_4_deg	17.032
r_dihedral_angle_3_deg	12.115
r_sphericity_bonded	7.518
r_dihedral_angle_1_deg	6.466
r_rigid_bond_restr	4.586
r_long_range_B_refined	2.049
r_long_range_B_other	2.049
r_angle_refined_deg	1.69
r_scangle_other	1.64
r_scbond_it	1.423
r_scbond_other	1.423
r_mcangle_it	1.248
r_mcangle_other	1.248
r_mcbond_it	0.988
r_mcbond_other	0.988
r_angle_other_deg	0.919
r_chiral_restr	0.101
r_bond_refined_d	0.014
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10834
Nucleic Acid Atoms
Solvent Atoms	1092
Heterogen Atoms	158

Software

Software
Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling