3QUF | pdb_00003quf

The structure of a family 1 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	4.6	294	0.1M sodium acetate pH 4.6, 2.5M ammonium sulfate, 1/10 papain, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.02	38.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.532	α = 90
b = 105.095	β = 90
c = 145.375	γ = 90

Symmetry
Space Group	C 2 2 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		2010-07-11	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97935, 0.97921	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	1.6	50	98.1	0.081	9	4.6	95082	95082		-3	20.1

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)
	1.6	1.63	95		0.582		4.2	4569

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	MAD	THROUGHOUT	1.7	48.27	79400	79400	3974	98.15	0.1523	0.1523	0.1509	0.1648	0.1804	0.1915	RANDOM	24.077

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]
1.42			-0.55		-0.87

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.17
r_dihedral_angle_4_deg	19.918
r_dihedral_angle_3_deg	13.703
r_dihedral_angle_1_deg	5.244
r_scangle_it	4.748
r_scbond_it	2.879
r_mcangle_it	1.743
r_angle_refined_deg	1.417
r_mcbond_it	0.945
r_angle_other_deg	0.895

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.17
r_dihedral_angle_4_deg	19.918
r_dihedral_angle_3_deg	13.703
r_dihedral_angle_1_deg	5.244
r_scangle_it	4.748
r_scbond_it	2.879
r_mcangle_it	1.743
r_angle_refined_deg	1.417
r_mcbond_it	0.945
r_angle_other_deg	0.895
r_mcbond_other	0.267
r_chiral_restr	0.092
r_bond_refined_d	0.015
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5996
Nucleic Acid Atoms
Solvent Atoms	825
Heterogen Atoms	33

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
MLPHARE	phasing
DM	phasing
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
SOLVE	phasing
RESOLVE	phasing
ARP/wARP	model building
CCP4	phasing
O	model building
Coot	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.