2F62 | pdb_00002f62

Crystal structure of Nucleoside 2-deoxyribosyltransferase from Trypanosoma brucei at 1.5 A resolution with (2-ETHYLPHENYL)METHANOL bound

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2A0K	pdb entry 2A0K

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	277	30 % PEG MME 2000, 0.2 ammonium sulfate, 0.1 sodium acetate trihydrate pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.56	51.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.614	α = 90
b = 75.913	β = 90.03
c = 85.957	γ = 90

Symmetry
Space Group	C 1 2 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	ADSC QUANTUM 315		2005-06-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.2	0.92020	ALS	8.2.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	86.68	0.034	19.4	3.2		49499			14.88

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.5	1.581	45.01		0.143	5.4	2	3728

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 (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	pdb entry 2A0K	1.5	30	49499	2675	86.68	0.16754	0.16754	0.1665	0.17	0.1863	0.17	RANDOM	12.409

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]
0.03			-0.11		0.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.468
r_dihedral_angle_4_deg	16.686
r_dihedral_angle_3_deg	10.853
r_dihedral_angle_1_deg	4.777
r_scangle_it	3.457
r_scbond_it	2.449
r_mcangle_it	1.723
r_mcbond_it	1.459
r_angle_refined_deg	0.968
r_nbtor_refined	0.306
r_nbd_refined	0.192
r_symmetry_vdw_refined	0.119
r_xyhbond_nbd_refined	0.088
r_symmetry_hbond_refined	0.077
r_chiral_restr	0.07
r_bond_refined_d	0.007
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2518
Nucleic Acid Atoms
Solvent Atoms	325
Heterogen Atoms	47

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
MOLREP	phasing