3CZ8

Crystal structure of putative sporulation-specific glycosylase ydhD from Bacillus subtilis

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	294	100mM Sodium cacodylate pH 7.0, 1.2M Sodium acetate, 10% Glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.72	54.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.965	α = 90
b = 84.965	β = 90
c = 188.041	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	77	CCD	MAR CCD 165 mm		2008-04-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.9793	APS	31-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	2.15	50	99.9	0.084	5.2	5.6		41723		-0.5	37.4

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	2.15	2.23	99.7		0.74	1.1	4.3

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	SAD	THROUGHOUT	2.2	20	37618	1212	99.99	0.19787	0.19597	0.25793	RANDOM	49.567

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]
0.65	0.32		0.65		-0.97

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.267
r_dihedral_angle_3_deg	17.194
r_dihedral_angle_4_deg	14.094
r_scangle_it	12.974
r_scbond_it	10.551
r_dihedral_angle_1_deg	9.453
r_mcangle_it	7.339
r_mcbond_it	5.503
r_angle_refined_deg	1.301
r_nbtor_refined	0.303
r_symmetry_hbond_refined	0.175
r_xyhbond_nbd_refined	0.163
r_nbd_refined	0.133
r_chiral_restr	0.101
r_symmetry_vdw_refined	0.083
r_bond_refined_d	0.009
r_gen_planes_refined	0.005
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	4768
Nucleic Acid Atoms
Solvent Atoms	192
Heterogen Atoms	48

Software

Software
Software Name	Purpose
SHELXD	phasing
REFMAC	refinement
MAR345	data collection
HKL-2000	data reduction
HKL-2000	data scaling