2YG8

Structure of an unusual 3-Methyladenine DNA Glycosylase II (Alka) from Deinococcus radiodurans

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				1 UL DROPS OF 10 MG/ML PROTEIN MIXED WITH A SOLUTION CONTAINING 1 M LICL2, 0.1 M MES PH 6.0 AND 10% PEG6000

Crystal Properties
Matthews coefficient	Solvent content
2.45	49.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 108.562	α = 90
b = 51.297	β = 99.76
c = 90.458	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 CCD	TOROIDAL MIRROR		M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29		ESRF	ID29

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	49.75	100	0.12	14.8	6.3		33423			12.7

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	2.11	100		0.39	5.1	6.4

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	NONE	2	49.75	31731	1693	99.98	0.16054	0.15828	0.20315	RANDOM	8.644

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]
0.04		0.02			-0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.459
r_dihedral_angle_4_deg	17.396
r_dihedral_angle_3_deg	13.494
r_dihedral_angle_1_deg	4.866
r_scangle_it	3.84
r_scbond_it	2.567
r_angle_refined_deg	1.43
r_mcangle_it	1.312
r_angle_other_deg	1.065
r_mcbond_it	1.002
r_symmetry_vdw_other	0.283
r_mcbond_other	0.216
r_nbd_refined	0.212
r_symmetry_hbond_refined	0.211
r_nbd_other	0.2
r_nbtor_refined	0.173
r_symmetry_vdw_refined	0.16
r_xyhbond_nbd_refined	0.146
r_nbtor_other	0.086
r_chiral_restr	0.084
r_bond_refined_d	0.016
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3073
Nucleic Acid Atoms
Solvent Atoms	613
Heterogen Atoms	22

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
SHARP	phasing