3BJE | pdb_00003bje

Crystal structure of Trypanosoma brucei nucleoside phosphorylase shows uridine phosphorylase activity

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	293	39% PEG 8000, 0.1 M Tris-HCl pH 8.5, 0.1 M Sodium phosphate monobasic, 10 mM Uridine, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.41	49.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.015	α = 90
b = 95.387	β = 105.91
c = 63.483	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	MARMOSAIC 325 mm CCD	Mirrors	2007-03-28	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.91724, 0.97910, 0.91160	SSRL	BL9-2

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	1.44	40	95.4	0.079	8.4	3.4	123263	123263			15.8

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	1.44	1.5	73.4		0.637	1.2	2.4	9430

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	1.44	35.38	123193	123193	6191	94.72	0.156	0.156	0.155	0.16	0.184	0.19	RANDOM	16.915

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]
-0.92		-0.62	-0.4		0.98

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.398
r_dihedral_angle_4_deg	16.468
r_dihedral_angle_3_deg	11.651
r_dihedral_angle_1_deg	5.856
r_scangle_it	4.3
r_scbond_it	2.948
r_mcangle_it	2.267
r_mcbond_it	1.722
r_angle_refined_deg	1.325
r_angle_other_deg	0.867
r_mcbond_other	0.477
r_symmetry_vdw_other	0.227
r_nbd_refined	0.208
r_nbd_other	0.203
r_nbtor_refined	0.174
r_xyhbond_nbd_refined	0.118
r_symmetry_hbond_refined	0.095
r_nbtor_other	0.083
r_chiral_restr	0.072
r_symmetry_vdw_refined	0.072
r_metal_ion_refined	0.048
r_bond_refined_d	0.01
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4984
Nucleic Acid Atoms
Solvent Atoms	501
Heterogen Atoms	45

Software

Software
Software Name	Purpose
Blu-Ice	data collection
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling