2BVL

Crystal structure of the catalytic domain of toxin B from Clostridium difficile in complex with UDP, Glc and manganese ion

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.5		pH 6.50

Crystal Properties
Matthews coefficient	Solvent content
2.48	50.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.01	α = 90
b = 95.797	β = 90
c = 112.915	γ = 90

Symmetry
Space Group	P 21 21 21

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	MARRESEARCH		2004-03-13	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA		SLS	X06SA

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	2.2	30	99.8	0.06	14.9	3.8		66915

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	2.29	99.9		0.29	4.6	3.8

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	OTHER	THROUGHOUT	2.2	30	34239	1117	99.8	0.198	0.197	0.244	RANDOM	41.66

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]
4.04			-1.01		-3.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.036
r_dihedral_angle_3_deg	16.159
r_dihedral_angle_4_deg	15.544
r_dihedral_angle_1_deg	5.95
r_scangle_it	2.846
r_scbond_it	1.819
r_angle_refined_deg	1.4
r_mcangle_it	1.116
r_mcbond_it	0.673
r_nbtor_refined	0.307
r_nbd_refined	0.207
r_symmetry_vdw_refined	0.199
r_symmetry_hbond_refined	0.184
r_xyhbond_nbd_refined	0.155
r_chiral_restr	0.091
r_bond_refined_d	0.012
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_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	4433
Nucleic Acid Atoms
Solvent Atoms	354
Heterogen Atoms	115

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling