1SMC | pdb_00001smc

Mycobacterium tuberculosis dUTPase complexed with dUTP in the absence of metal ion.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		M. tuberculosis dUTPase complexed with dUMP and magnesium.

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	298	PEG 3350, ammonium nitrate, Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.51	50.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.595	α = 90
b = 77.697	β = 90
c = 94.781	γ = 90

Symmetry
Space Group	P 21 21 21

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	ADSC QUANTUM 4	mirrors	2002-11-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-D	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	2.05	80	100	0.109	22.7	13.1	27903	27903			34.9

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	2.05	2.12	100		0.453	5.8	11.1	2746

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	FOURIER SYNTHESIS	THROUGHOUT	M. tuberculosis dUTPase complexed with dUMP and magnesium.	2.1	50	23083	23083	2525	98.86	0.16959	0.16959	0.16549	0.18	0.20675	0.22	RANDOM	19.246

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]
-0.59			-1.33		1.92

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.375
r_scangle_it	4.932
r_scbond_it	2.921
r_angle_refined_deg	2.246
r_mcangle_it	1.791
r_angle_other_deg	1.091
r_mcbond_it	1.033
r_symmetry_vdw_other	0.353
r_nbd_other	0.265
r_symmetry_hbond_refined	0.19
r_nbd_refined	0.188
r_symmetry_vdw_refined	0.163
r_nbtor_other	0.161
r_xyhbond_nbd_refined	0.157
r_chiral_restr	0.114
r_bond_refined_d	0.019
r_gen_planes_refined	0.008
r_gen_planes_other	0.005
r_bond_other_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2928
Nucleic Acid Atoms
Solvent Atoms	220
Heterogen Atoms	112

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing