3BVS

Crystal Structure of Bacillus cereus Alkylpurine DNA Glycosylase AlkD

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	294	85 mM HEPES pH 7.5, 15% PEG 4000, 17% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
3.08	60.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.917	α = 90
b = 77.917	β = 90
c = 55.102	γ = 90

Symmetry
Space Group	P 43

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	110	CCD	MARMOSAIC 225 mm CCD	Oxford Danfysik toroidal focusing mirror	2006-12-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	1.0000	APS	21-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.08	29.5	99.1	0.046	0.046	26.9	7.1	19887	19887

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.08	2.08	95.3		0.531	0.531	3.4	6.2

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.1	50	18356	18356	968	99.49	0.18974	0.18782	0.22718	RANDOM	51.956

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			1		-2

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.549
r_dihedral_angle_4_deg	20.291
r_dihedral_angle_3_deg	17.876
r_dihedral_angle_1_deg	6.248
r_scangle_it	3.111
r_scbond_it	2.116
r_angle_refined_deg	1.571
r_mcangle_it	1.226
r_mcbond_it	0.685
r_nbtor_refined	0.311
r_nbd_refined	0.229
r_symmetry_hbond_refined	0.217
r_symmetry_vdw_refined	0.21
r_xyhbond_nbd_refined	0.153
r_chiral_restr	0.106
r_bond_refined_d	0.018
r_gen_planes_refined	0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1891
Nucleic Acid Atoms
Solvent Atoms	81
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345dtb	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHARP	phasing