3OMB | pdb_00003omb

Crystal structure of extracellular solute-binding protein from Bifidobacterium longum subsp. infantis

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	297	0.1M Bis-Tris, 0.2M MgCl2, 25% PEG3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K

Crystal Properties
Matthews coefficient	Solvent content
1.97	37.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.949	α = 90
b = 70.099	β = 90
c = 122.177	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	ADSC QUANTUM 315r		2010-04-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97929	APS	19-ID

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	2.1	50	100	0.117	23.8	7.1	28267	28262		-3	24.4

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)
	2.1	2.14	100		0.509	4.4	7.2	1393

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	2.1	50	28206	28206	1420	99.7	0.1547	0.1547	0.1508	0.1571	0.2269	0.2295	RANDOM	27.254

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]
0.13			-0.05		-0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.482
r_dihedral_angle_4_deg	17.928
r_dihedral_angle_3_deg	15.36
r_dihedral_angle_1_deg	5.594
r_scangle_it	4.581
r_scbond_it	2.895
r_mcangle_it	1.725
r_rigid_bond_restr	1.434
r_angle_refined_deg	1.337
r_mcbond_it	0.942

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.482
r_dihedral_angle_4_deg	17.928
r_dihedral_angle_3_deg	15.36
r_dihedral_angle_1_deg	5.594
r_scangle_it	4.581
r_scbond_it	2.895
r_mcangle_it	1.725
r_rigid_bond_restr	1.434
r_angle_refined_deg	1.337
r_mcbond_it	0.942
r_chiral_restr	0.089
r_bond_refined_d	0.013
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3945
Nucleic Acid Atoms
Solvent Atoms	360
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
MLPHARE	phasing
DM	phasing
RESOLVE	phasing
Coot	model building
ARP/wARP	model building

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.