3D33

Crystal structure of a duf3244 family protein with an immunoglobulin-like beta-sandwich fold (bvu_0276) from bacteroides vulgatus atcc 8482 at 1.70 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.9	277	0.2000M MgFormate, 20.0000% PEG-3350, No Buffer pH 5.9, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.42	49.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.562	α = 90
b = 55.179	β = 94.31
c = 47.116	γ = 90

Symmetry
Space Group	P 1 21 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 325 mm CCD	Flat mirror (vertical focusing)	2008-04-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1		SSRL	BL11-1

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	1.7	28.677	99.6	0.098	0.098	4.6	7.4		25116			24.306

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	1.7	1.74	95.7		0.871	0.871	0.9	7	1763

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	1.7	28.677	25099	1283	99.63	0.176	0.174	0.22	RANDOM	18.342

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]
0.37		-0.05	0.32		-0.7

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.188
r_dihedral_angle_4_deg	16.805
r_dihedral_angle_3_deg	12.758
r_dihedral_angle_1_deg	6.224
r_scangle_it	5.982
r_scbond_it	4.374
r_mcangle_it	2.717
r_mcbond_it	1.914
r_angle_refined_deg	1.494
r_angle_other_deg	0.845
r_mcbond_other	0.552
r_nbd_other	0.21
r_nbd_refined	0.193
r_symmetry_vdw_other	0.18
r_nbtor_refined	0.175
r_symmetry_hbond_refined	0.171
r_symmetry_vdw_refined	0.134
r_xyhbond_nbd_refined	0.116
r_nbtor_other	0.089
r_chiral_restr	0.087
r_bond_refined_d	0.015
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1439
Nucleic Acid Atoms
Solvent Atoms	283
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SOLVE	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction