2H56

Crystal structure of DNA-3-methyladenine glycosidase (10174367) from Bacillus halodurans at 2.55 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP, NANODROP	7.1	277	0.2M NaF, 20.0% PEG-3350, No Buffer, pH 7.1, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.2	61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 141.752	α = 90
b = 141.752	β = 90
c = 85.949	γ = 120

Symmetry
Space Group	P 65

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		2005-09-10	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.2	1.0163, 0.9798	ALS	8.2.2

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	2.54	46.42	93.4	0.091	15.62	6.49		31756			54.685

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	2.54	2.63	86.1		0.39	2	2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MAD	THROUGHOUT	2.55	46.4	31729	1606	98	0.198	0.196	0.246	RANDOM	57.814

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]
1.61	0.81		1.61		-2.42

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.165
r_dihedral_angle_3_deg	16.788
r_dihedral_angle_4_deg	16.676
r_scangle_it	7.528
r_dihedral_angle_1_deg	5.808
r_scbond_it	5.484
r_mcangle_it	2.885
r_mcbond_it	1.693
r_angle_refined_deg	1.418
r_angle_other_deg	0.93
r_mcbond_other	0.367
r_symmetry_vdw_other	0.238
r_nbd_refined	0.236
r_symmetry_hbond_refined	0.197
r_nbtor_refined	0.194
r_nbd_other	0.181
r_xyhbond_nbd_refined	0.173
r_symmetry_vdw_refined	0.152
r_nbtor_other	0.088
r_chiral_restr	0.073
r_xyhbond_nbd_other	0.026
r_bond_refined_d	0.014
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4815
Nucleic Acid Atoms
Solvent Atoms	40
Heterogen Atoms

Software

Software
Software Name	Purpose
MolProbity	model building
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELX	phasing
autoSHARP	phasing