2PY4

Full length structure of the Mycobacterium tuberculosis dUTPase complexed with magnesium and alpha,beta-imido-dUTP.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1MQ7	pdb entry 1MQ7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	298	1.5M ammonium sulfate, 0.1M Tris/HCl, 12% glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
1.98	38.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.591	α = 90
b = 54.591	β = 90
c = 83.051	γ = 120

Symmetry
Space Group	P 63

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	RIGAKU RAXIS II			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.5418

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	1.49	20	94.1	4.1	24.57	3.95	21589	21589		-3	19.3

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	1.49	1.58	70.5		34.8	3.3	2.3	2595

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entry 1MQ7	1.49	19.44	20480	20480	1109	94.09	0.14553	0.1442	0.16997	RANDOM	18.838

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]
0.06	0.03		0.06		-0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.284
r_dihedral_angle_4_deg	16.368
r_dihedral_angle_3_deg	9.073
r_dihedral_angle_1_deg	6.274
r_scangle_it	6.054
r_scbond_it	4.976
r_mcangle_it	3.137
r_mcbond_it	2.164
r_angle_refined_deg	1.992
r_nbtor_refined	0.321

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.284
r_dihedral_angle_4_deg	16.368
r_dihedral_angle_3_deg	9.073
r_dihedral_angle_1_deg	6.274
r_scangle_it	6.054
r_scbond_it	4.976
r_mcangle_it	3.137
r_mcbond_it	2.164
r_angle_refined_deg	1.992
r_nbtor_refined	0.321
r_nbd_refined	0.213
r_symmetry_vdw_refined	0.188
r_chiral_restr	0.148
r_symmetry_hbond_refined	0.147
r_xyhbond_nbd_refined	0.108
r_bond_refined_d	0.02
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1081
Nucleic Acid Atoms
Solvent Atoms	132
Heterogen Atoms	37

Software

Software
Software Name	Purpose
REFMAC	refinement
START	data collection
XDS	data reduction
XSCALE	data scaling
MOLREP	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.