1PU8

Crystal structure of H.pylori 3-methyladenine DNA glycosylase (MagIII) bound to 1,N6-ethenoadenine

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	277	PEG 4000, HEPES, MPD, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 146.605	α = 90
b = 44.399	β = 106.4
c = 81.516	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	110	IMAGE PLATE	MARRESEARCH		2002-09-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	SIEMENS	1.542

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	2.13	50	99.8	0.084	11.5	2.9	28226	28226			23

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	2.13	2.23	99.6		0.369	2.5	2.9	2783

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1PU6	2.13	50	26792	26792	1434	98.19	0.20369	0.20369	0.20228	0.22992	RANDOM	13.758

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		-0.44	0.37		-0.56

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.211
r_scangle_it	3.052
r_scbond_it	2.032
r_angle_refined_deg	1.508
r_mcangle_it	1.162
r_mcbond_it	0.627
r_symmetry_vdw_refined	0.241
r_nbd_refined	0.214
r_symmetry_hbond_refined	0.156
r_xyhbond_nbd_refined	0.121
r_chiral_restr	0.092
r_bond_refined_d	0.013
r_gen_planes_refined	0.005
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3467
Nucleic Acid Atoms
Solvent Atoms	161
Heterogen Atoms	32

Software

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