3H6D

Structure of the mycobacterium tuberculosis DUTPase D28N mutant

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2PY4	PDB ENTRY 2PY4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8.5	298	1.45 M Ammonium sulphate, 50 mM Tris, 12% Glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.05	39.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.228	α = 90
b = 55.228	β = 90
c = 83.65	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	CCD	MARMOSAIC 225 mm CCD	MIRRORS	2008-12-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X12		EMBL/DESY, HAMBURG	X12

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	1.8	20	99.9	0.069	14.58	3.39		13348		-3	26.12

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	1.8	1.85	99.2		0.471	2.41	2.54

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2PY4	1.8	19.16	12638	688	99.14	0.1602	0.15765	0.20733	RANDOM	16.224

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]
0.72	0.36		0.72		-1.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.503
r_dihedral_angle_4_deg	17.386
r_dihedral_angle_3_deg	11.635
r_dihedral_angle_1_deg	6.294
r_scangle_it	4.979
r_scbond_it	3.097
r_angle_other_deg	2.592
r_mcangle_it	1.866
r_angle_refined_deg	1.741
r_mcbond_it	1.138
r_mcbond_other	0.41
r_symmetry_vdw_other	0.28
r_symmetry_hbond_refined	0.197
r_xyhbond_nbd_refined	0.16
r_symmetry_vdw_refined	0.141
r_chiral_restr	0.091
r_bond_refined_d	0.015
r_gen_planes_refined	0.009
r_gen_planes_other	0.001
r_bond_other_d
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1046
Nucleic Acid Atoms
Solvent Atoms	89
Heterogen Atoms	45

Software

Software
Software Name	Purpose
XSCALE	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction