3C2U

Structure of the two subsite D-xylosidase from Selenomonas ruminantium in complex with 1,3-bis[tris(hydroxymethyl)methylamino]propane

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	298	4 L of protein solution (1.6 mg/mL in 0.1 M BTP-HCl pH 8.0) mixed with 1 L of the well solution containing 22-25% (w/v) PEG 1100 monomethyl ether in 0.1M BTP-HCl, pH 8.0., VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.579	α = 67.84
b = 84.401	β = 81.31
c = 94.039	γ = 75.08

Symmetry
Space Group	P 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	MARMOSAIC 225 mm CCD		2005-07-19	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 5ID-B	0.9784, 0.9786, 0.9632	APS	5ID-B

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	1.2	100	94.5	0.063	12.55	4.48	667241	630354		-3	17.2

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	1.24	91.4		0.382	3.65	3.89	57143

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	1.3	87.04	474622	24998	95.29	0.13572	0.13427	0.16303	RANDOM	11.81

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]
-0.46	1.1	-0.41	-0.11	0.12	0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.865
r_dihedral_angle_4_deg	17.043
r_dihedral_angle_3_deg	11.777
r_sphericity_free	9.143
r_dihedral_angle_1_deg	6.787
r_sphericity_bonded	4.398
r_scangle_it	3.675
r_scbond_it	2.965
r_mcangle_it	2.079
r_mcbond_it	1.758
r_angle_refined_deg	1.656
r_rigid_bond_restr	1.504
r_angle_other_deg	1.091
r_mcbond_other	0.849
r_symmetry_vdw_other	0.246
r_nbd_refined	0.2
r_nbd_other	0.193
r_nbtor_refined	0.187
r_symmetry_hbond_refined	0.166
r_xyhbond_nbd_refined	0.142
r_symmetry_vdw_refined	0.112
r_chiral_restr	0.11
r_nbtor_other	0.088
r_bond_refined_d	0.015
r_gen_planes_refined	0.01
r_bond_other_d	0.001
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

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	17832
Nucleic Acid Atoms
Solvent Atoms	2050
Heterogen Atoms	81

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345	data collection
XDS	data reduction
XDS	data scaling
XSCALE	data scaling
SnB	phasing