2J0F

Structural basis for non-competitive product inhibition in human thymidine phosphorylase: implication for drug design

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7		20% GLYCEROL, 20% PEG3350, pH 7.00

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 103.078	α = 90
b = 76.087	β = 98.61
c = 99.575	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	IMAGE PLATE	MARRESEARCH		2005-10-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	MAR345

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	2.3	30	99.3	0.12	18.2	8.6		63091		2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.38	99			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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1UOU	2.31	102.06	63091	3368	99.3	0.248	0.246	0.287	RANDOM	12.84

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]
-2.52		0.3	-1.2		3.81

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.025
r_dihedral_angle_4_deg	17.691
r_dihedral_angle_3_deg	16.279
r_dihedral_angle_1_deg	5.518
r_scangle_it	5.404
r_scbond_it	2.888
r_mcangle_it	1.461
r_angle_refined_deg	1.247
r_mcbond_it	0.829
r_symmetry_hbond_refined	0.362
r_symmetry_vdw_refined	0.342
r_nbtor_refined	0.292
r_nbd_refined	0.206
r_xyhbond_nbd_refined	0.173
r_chiral_restr	0.076
r_bond_refined_d	0.009
r_gen_planes_refined	0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13036
Nucleic Acid Atoms
Solvent Atoms	450
Heterogen Atoms	27

Software

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