3KLB

Crystal structure of Putative Flavoprotein in Complex with FMN (YP_213683.1) from Bacteroides fragilis NCTC 9343 at 1.75 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	10.0000% Glycerol, 1.2600M sodium citrate, 0.1M HEPES pH 7.5, Additive: 0.001 M FMN, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.06	59.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.764	α = 90
b = 96.764	β = 90
c = 47.882	γ = 90

Symmetry
Space Group	P 43 21 2

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 collimating mirror, toroid focusing mirror	2009-05-13	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.91162,0.97939,0.97927	SSRL	BL9-2

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	1.75	27.832	99.2	0.057	17.33			23388		-3	22.346

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	1.75	1.81	94.2		0.732	1.9

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	1.75	27.832	23346	1196	99.76	0.15	0.148	0.179	RANDOM	29.843

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]
-0.94			-0.94		1.88

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.974
r_dihedral_angle_4_deg	14.835
r_dihedral_angle_3_deg	12.388
r_dihedral_angle_1_deg	6.067
r_scangle_it	5.997
r_scbond_it	4.327
r_mcangle_it	2.803
r_mcbond_it	1.722
r_angle_refined_deg	1.548
r_angle_other_deg	0.961
r_mcbond_other	0.534
r_symmetry_vdw_refined	0.317
r_nbd_refined	0.217
r_nbd_other	0.201
r_symmetry_vdw_other	0.191
r_nbtor_refined	0.186
r_xyhbond_nbd_refined	0.164
r_symmetry_hbond_refined	0.114
r_chiral_restr	0.101
r_metal_ion_refined	0.086
r_symmetry_metal_ion_refined	0.086
r_nbtor_other	0.083
r_bond_refined_d	0.017
r_gen_planes_refined	0.009
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1258
Nucleic Acid Atoms
Solvent Atoms	175
Heterogen Atoms	84

Software

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