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Crystal structure of putative oxidoreductase (YP_213212.1) from Bacteroides fragilis NCTC 9343 at 1.99 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	277	10.0000% iso-Propanol, 20.0000% PEG-4000, 0.1M HEPES pH 7.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.37	α = 90
b = 80.82	β = 90
c = 101.47	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	MARMOSAIC 325 mm CCD	Flat mirror (vertical focusing)	2008-08-07	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)	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	1.99	28.76	96.8	0.107	7.12	4.84		39369		-3	23.863

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	2.01	2.08	84.7		0.657	1.6

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	1.99	28.76	39318	1974	99.31	0.171	0.169	0.224	RANDOM	27.7

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]
3.67			-1.59		-2.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.15
r_dihedral_angle_3_deg	13.138
r_dihedral_angle_4_deg	11.9
r_scangle_it	7.282
r_scbond_it	5.687
r_dihedral_angle_1_deg	3.737
r_mcangle_it	2.941
r_mcbond_it	2.211
r_angle_refined_deg	1.66
r_angle_other_deg	0.989
r_mcbond_other	0.584
r_symmetry_vdw_other	0.249
r_nbd_refined	0.208
r_nbd_other	0.205
r_symmetry_hbond_refined	0.19
r_nbtor_refined	0.186
r_xyhbond_nbd_refined	0.162
r_chiral_restr	0.098
r_nbtor_other	0.089
r_symmetry_vdw_refined	0.078
r_bond_refined_d	0.018
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3972
Nucleic Acid Atoms
Solvent Atoms	364
Heterogen Atoms	62

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHARP	phasing