4EAD | pdb_00004ead

Thymidine phosphorylase from E.coli with 3'-azido-2'-fluoro-dideoxyuridine

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2TPT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1			273	COUNTER DIFFUSION, LIQUID DIFFUSION, temperature 273K

Crystal Properties
Matthews coefficient	Solvent content
3.02	59.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 129.862	α = 90
b = 129.862	β = 90
c = 67.656	γ = 90

Symmetry
Space Group	P 43 21 2

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	RAYONIX MX225HE	MIRRORS	2011-10-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU		SPring-8	BL41XU

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	1.5	30	99.8	0.062				92521

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	1.5	1.51	99.7		0.519	0.519	3.24

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	2TPT	1.5	16	87704	4617	99.8	0.147	0.145	0.15	0.192	0.19	RANDOM	26.83

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]
-0.2			-0.2		0.39

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.143
r_sphericity_free	32.614
r_dihedral_angle_4_deg	16.935
r_sphericity_bonded	16.431
r_dihedral_angle_3_deg	15.564
r_dihedral_angle_1_deg	6.111
r_rigid_bond_restr	2.177
r_angle_refined_deg	1.443
r_angle_other_deg	0.914
r_chiral_restr	0.083
r_bond_refined_d	0.008
r_gen_planes_refined	0.005
r_bond_other_d	0.004
r_gen_planes_other
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3306
Nucleic Acid Atoms
Solvent Atoms	520
Heterogen Atoms	73

Software

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