4DLC | pdb_00004dlc

Crystal Structure of Trypanosoma brucei dUTPase with dUMP, MgF3- transition state analogue, and Mg2+

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	8.5	290	0.2 M sodium/potassium tartrate, 0.1 M Bis-Tris propane, pH 8.5, 20% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.28	α = 90
b = 68.28	β = 90
c = 123.66	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 6M		2011-07-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.976	Diamond	I03

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	1.759	48.281	99.8	0.073	0.073	22	12.7	29775	29775	1	1	24.1

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	1.759	1.8	99.8		0.781	0.781	1	12.2	2169

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	1.759	48.28	29775	29775	1495	99.86	0.1668	0.1668	0.1654	0.17	0.194	0.2	RANDOM	26.3871

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]
0.61			0.61		-1.22

RMS Deviations
Key	Refinement Restraint Deviation
r_scbond_it	36.964
r_scangle_it	35.581
r_dihedral_angle_2_deg	35.492
r_dihedral_angle_4_deg	13.239
r_dihedral_angle_3_deg	11.072
r_mcangle_it	8.521
r_mcbond_it	6.807
r_dihedral_angle_1_deg	5.218
r_angle_refined_deg	1.41
r_mcbond_other	1.199

RMS Deviations
Key	Refinement Restraint Deviation
r_scbond_it	36.964
r_scangle_it	35.581
r_dihedral_angle_2_deg	35.492
r_dihedral_angle_4_deg	13.239
r_dihedral_angle_3_deg	11.072
r_mcangle_it	8.521
r_mcbond_it	6.807
r_dihedral_angle_1_deg	5.218
r_angle_refined_deg	1.41
r_mcbond_other	1.199
r_angle_other_deg	0.935
r_chiral_restr	0.086
r_bond_refined_d	0.015
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	1750
Nucleic Acid Atoms
Solvent Atoms	159
Heterogen Atoms	27

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.