3I93 | pdb_00003i93

Crystal structure of Mycobacterium tuberculosis dUTPase STOP138T mutant

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3HZA	PDB entry 3HZA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	1.3 M Ammonium sulfate, 50 mM Tris-HCl, 12 % Glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.16	42.95

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	CCD	MARMOSAIC 225 mm CCD	mirrors	2008-12-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X12	0.97861	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	99.7	0.067	17.77	5.52		13306		-3	28.165

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		0.503	2.85	4.15	972

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	PDB entry 3HZA	1.8	19.44	11999	638	96.92	0.16623	0.16423	0.18	0.20611	0.21	RANDOM	15.958

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]
0.08	0.04		0.08		-0.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.01
r_dihedral_angle_4_deg	21.334
r_dihedral_angle_3_deg	12.003
r_dihedral_angle_1_deg	6.754
r_scangle_it	4.179
r_scbond_it	2.705
r_mcangle_it	1.693
r_angle_refined_deg	1.549
r_mcbond_it	1.017
r_angle_other_deg	0.616
r_mcbond_other	0.324
r_chiral_restr	0.077
r_bond_refined_d	0.014
r_gen_planes_refined	0.006
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_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
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	1006
Nucleic Acid Atoms
Solvent Atoms	105
Heterogen Atoms	37

Software

Software
Software Name	Purpose
MAR345	data collection
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling