2B06 | pdb_00002b06

Crystal structure of the MutT/nudix family protein from Streptococcus pneumoniae

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	298	0.1M Tris/HCl, 0.2M MgSO4, 25% PEG3350, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
1.94	36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.85	α = 90
b = 64.99	β = 127.6
c = 41.779	γ = 90

Symmetry
Space Group	C 1 2 1

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 315	mirrors	2005-04-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.9798	APS	19-ID

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	1.4	50	94.5	0.045	22.8	2.4		25116	2	2	22

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	1.4	1.45	79.5		0.157	3.3	2.1	5382

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	THROUGHOUT	1.4	40.69	26059	25116	1318	96.38	0.19046	0.19046	0.1889	0.1899	0.21923	0.1809	RANDOM	19.71

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]
-1.47		-1.01	1.29		-1.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.442
r_dihedral_angle_4_deg	21.294
r_dihedral_angle_3_deg	12.66
r_dihedral_angle_1_deg	5.627
r_scangle_it	2.77
r_scbond_it	1.927
r_mcangle_it	1.245
r_angle_refined_deg	1.215
r_mcbond_it	0.786
r_nbtor_refined	0.312
r_nbd_refined	0.198
r_symmetry_vdw_refined	0.196
r_xyhbond_nbd_refined	0.173
r_symmetry_hbond_refined	0.143
r_chiral_restr	0.082
r_metal_ion_refined	0.011
r_bond_refined_d	0.008
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1222
Nucleic Acid Atoms
Solvent Atoms	227
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-2000	data scaling
HKL-3000	phasing