3KEZ | pdb_00003kez

Crystal structure of Putative sugar binding protein (YP_001299726.1) from Bacteroides vulgatus ATCC 8482 at 1.90 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.9	277	0.2000M (NH4)2HPO4, 20.0000% PEG-3350, No Buffer pH 7.9, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.498	α = 90
b = 91.088	β = 90
c = 117.861	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	2009-05-15	M	SINGLE WAVELENGTH

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

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	1.9	29.748	99.3	0.152	0.152	8.9	4.8		75204			15.886

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	1.9	1.95	92.9		0.643	0.643	1	3.5	5109

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	SAD	THROUGHOUT	1.9	29.748	75129	3785	99.31	0.155	0.152	0.17	0.204	0.22	RANDOM	14.755

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]
-0.24			-0.83		1.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.428
r_dihedral_angle_4_deg	19.059
r_dihedral_angle_3_deg	12.908
r_scangle_it	6.252
r_dihedral_angle_1_deg	6.089
r_scbond_it	4.633
r_mcangle_it	2.596
r_mcbond_it	1.775
r_angle_refined_deg	1.441
r_angle_other_deg	0.946

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.428
r_dihedral_angle_4_deg	19.059
r_dihedral_angle_3_deg	12.908
r_scangle_it	6.252
r_dihedral_angle_1_deg	6.089
r_scbond_it	4.633
r_mcangle_it	2.596
r_mcbond_it	1.775
r_angle_refined_deg	1.441
r_angle_other_deg	0.946
r_mcbond_other	0.567
r_chiral_restr	0.092
r_bond_refined_d	0.016
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7110
Nucleic Acid Atoms
Solvent Atoms	998
Heterogen Atoms	72

Software

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

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.