1RXU | pdb_00001rxu

E. coli uridine phosphorylase: thymidine phosphate complex

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		A SINGLE HEXAMER (CHAINS ABCDEF) OF THE 5-FLUOROURACIL PHOSPHATE UP COMPLEX MODEL.

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH METHOD UNDER OIL	7.5	289	TRIS HCL, PEG4000, POTASSIUM ACETATE, THYMIDINE, POTASSIUM PHOSPHATE, pH 7.50, BATCH METHOD UNDER OIL, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.2	43.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 156.244	α = 90
b = 97.655	β = 118.23
c = 161.453	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	115	IMAGE PLATE	MARRESEARCH	OSMIC	2002-08-06	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	3.1	41.89	98.2	0.158	4.7	2.6	76410	76410			61.398

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	3.1	3.26	97		0.529	1.4	2.5	5116

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	A SINGLE HEXAMER (CHAINS ABCDEF) OF THE 5-FLUOROURACIL PHOSPHATE UP COMPLEX MODEL.	3.1	25	72181	72181	3824	97.52	0.21256	0.21256	0.21167	0.19	0.22945	0.21	RANDOM	26.192

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]
-0.81		0.33	1.57		-0.45

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.707
r_scangle_it	4.054
r_scbond_it	2.157
r_mcangle_it	1.447
r_angle_refined_deg	1.162
r_mcbond_it	0.715
r_symmetry_vdw_refined	0.648
r_symmetry_hbond_refined	0.451
r_nbd_refined	0.208
r_xyhbond_nbd_refined	0.142
r_metal_ion_refined	0.123
r_chiral_restr	0.093
r_bond_refined_d	0.01
r_gen_planes_refined	0.003
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_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	33840
Nucleic Acid Atoms
Solvent Atoms	1062
Heterogen Atoms	405

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing
REFMAC	refinement
CCP4	data scaling