4DL8 | pdb_00004dl8

Crystal structure of Trypanosoma brucei dUTPase with dUMP, planar [AlF3-OPO3] transition state analogue, Mg2+, and Na+

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4DKB	PDB ENTRY 4DKB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	290	0.2 M sodium sulfate, 0.1 M Bis-Tris propane, pH 6.5, 20% w/v PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.59	α = 90
b = 68.59	β = 90
c = 123.759	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	PIXEL	DECTRIS PILATUS 2M		2011-01-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.917	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.698	28.203	99.7	0.078	0.078	23.5	15.7	33398	33398	1	1	23.8

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	1.698	1.79	98.4		0.923	0.923	0.8	15.7	4710

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	REFINED 4DKB	THROUGHOUT	PDB ENTRY 4DKB	1.698	28.2	33398	33293	1661	99.7	0.1681	0.1681	0.1667	0.17	0.1944	0.2	RANDOM	25.9297

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]
0.5			0.5		-1.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.527
r_scbond_it	21.286
r_mcbond_it	20.91
r_mcangle_it	18.155
r_scangle_it	17.605
r_dihedral_angle_4_deg	13.339
r_dihedral_angle_3_deg	11.825
r_dihedral_angle_1_deg	5.106
r_angle_refined_deg	1.416
r_angle_other_deg	0.944

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.527
r_scbond_it	21.286
r_mcbond_it	20.91
r_mcangle_it	18.155
r_scangle_it	17.605
r_dihedral_angle_4_deg	13.339
r_dihedral_angle_3_deg	11.825
r_dihedral_angle_1_deg	5.106
r_angle_refined_deg	1.416
r_angle_other_deg	0.944
r_mcbond_other	0.606
r_chiral_restr	0.091
r_bond_refined_d	0.016
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1764
Nucleic Acid Atoms
Solvent Atoms	166
Heterogen Atoms	32

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XSCALE	data scaling
REFMAC	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.