4AQ4 | pdb_00004aq4

substrate bound sn-glycerol-3-phosphate binding periplasmic protein ugpB from Escherichia coli

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.5		VAPOUR DIFFUSION (1:1 MIX): 5 MM COBALT(II) CHLORIDE, 5 MM NICKEL(II) CHLORIDE, 5 MM CADMIUM CHLORIDE, 5 MM MAGNESIUM CHLORIDE, 0.1 M HEPES PH 7.5, 12% W/V POLYETHYLENE GLYCOL 3350, 0.3% N-OCTYL-BETA-D-GLUCOSIDE, 5MM SN- GLYCEROL-3-PHOSPHATE, 1% GLYCEROL, 90 MG/ML PROTEIN

Crystal Properties
Matthews coefficient	Solvent content
2.67	54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.346	α = 90
b = 49.346	β = 90
c = 406.894	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 225 mm CCD		2011-01-18	M	SINGLE WAVELENGTH
2	1	x-ray		CCD	MARMOSAIC 225 mm CCD			M

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1		BESSY	14.1
2	SYNCHROTRON	BESSY BEAMLINE 14.2		BESSY	14.2

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	1.8	50	99.7	0.06	18.8	5.1		88817		3	19.59

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	1.8	1.91	98.5		0.4	3.9	5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	SAD	NONE	1.8	46.372	2	88812	4464	99.75	0.1641	0.1626	0.17	0.1922	0.19

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]
1.1376			1.1376		-2.2751

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	13.615
f_angle_d	1.019
f_chiral_restr	0.07
f_bond_d	0.006
f_plane_restr	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3274
Nucleic Acid Atoms
Solvent Atoms	335
Heterogen Atoms	25

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	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.