3MYV | pdb_00003myv

Crystal structure of a SusD superfamily protein (BVU_0732) from Bacteroides vulgatus ATCC 8482 at 1.80 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.7	277	22.5000% polyethylene glycol 3350, 0.2000M di-sodium hydrogen phosphate, 0.1M HEPES pH 6.7, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.136	α = 90
b = 83.639	β = 90
c = 223.303	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 collimating mirror, toroid focusing mirror	2009-11-06	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.91837,0.97954,0.97934	SSRL	BL9-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.8	74.434	99.9	0.112	6.4	3.7		96603			18.505

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)
	1.8	1.9	99.9		0.59	0.59	1.9	3.7	13961

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	1.8	74.434	96490	4830	99.74	0.153	0.151	0.16	0.19	0.2	RANDOM	22.387

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]
1.33			-0.56		-0.77

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.815
r_dihedral_angle_4_deg	14.003
r_dihedral_angle_3_deg	12.674
r_dihedral_angle_1_deg	5.751
r_scangle_it	5.268
r_scbond_it	3.778
r_mcangle_it	2.165
r_mcbond_it	1.455
r_angle_refined_deg	1.272
r_angle_other_deg	0.882

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.815
r_dihedral_angle_4_deg	14.003
r_dihedral_angle_3_deg	12.674
r_dihedral_angle_1_deg	5.751
r_scangle_it	5.268
r_scbond_it	3.778
r_mcangle_it	2.165
r_mcbond_it	1.455
r_angle_refined_deg	1.272
r_angle_other_deg	0.882
r_mcbond_other	0.454
r_chiral_restr	0.079
r_bond_refined_d	0.013
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	7018
Nucleic Acid Atoms
Solvent Atoms	1232
Heterogen Atoms	78

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.