1T0U

Crystal structure of E.coli uridine phosphorylase at 2.2 A resolution (Type-A Native)

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	298	Tris-HCl, PEG, Sodium Acetate, pH 8.50, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.02	38.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 151.336	α = 90
b = 151.336	β = 90
c = 48.366	γ = 120

Symmetry
Space Group	H 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	200	IMAGE PLATE	MARRESEARCH		1998-11-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.5418

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	2.2	29.11	99.8	0.086	15.08	3.77	188478	20914		0.5	25.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.28	100		0.281	4.42	3.65

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SIR(URANYL DERIVATIVE)	THROUGHOUT	2.2	29.11	20914	19837	1075	99.8	0.163	0.163	0.161	0.203	RANDOM	20.73

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]
-0.51	-0.25		-0.51		0.76

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	18.404
r_scangle_it	4.624
r_dihedral_angle_1_deg	4.156
r_scbond_it	2.795
r_angle_refined_deg	1.831
r_mcangle_it	1.79
r_angle_other_deg	1.452
r_mcbond_it	0.97
r_symmetry_vdw_other	0.342
r_symmetry_vdw_refined	0.258
r_nbd_other	0.237
r_nbd_refined	0.222
r_xyhbond_nbd_refined	0.175
r_symmetry_hbond_refined	0.132
r_chiral_restr	0.116
r_xyhbond_nbd_other	0.111
r_nbtor_other	0.05
r_bond_refined_d	0.021
r_gen_planes_refined	0.008
r_gen_planes_other	0.008
r_bond_other_d
r_dihedral_angle_2_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3511
Nucleic Acid Atoms
Solvent Atoms	247
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MLPHARE	phasing
REFMAC	refinement