5JBF

4,6-alpha-glucanotransferase GTFB (D1015N mutant) from Lactobacillus reuteri 121 complexed with maltopentaose

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3KLK	PDB ID 3KLK domains A, B, C, IV

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	293	PEG3350, NaCl, (NH4)2SO4

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 219.484	α = 90
b = 58.139	β = 114.36
c = 150.382	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS3 2M		2015-05-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.8729	ESRF	ID23-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	2.19	48.02	90.3	0.061	0.996	8.2	2.2		80800

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	2.19	2.23	90.5		0.354		2.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ID 3KLK domains A, B, C, IV	2.19	48.02	76747	4021	90.19	0.1959	0.1938	0.2375	RANDOM	42.342

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]
0.61		1.44	-2.32		0.29

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.762
r_dihedral_angle_4_deg	17.229
r_dihedral_angle_3_deg	13.766
r_dihedral_angle_1_deg	6.544
r_angle_refined_deg	1.455
r_mcangle_it	1.195
r_angle_other_deg	1.104
r_mcbond_it	0.714
r_mcbond_other	0.714
r_chiral_restr	0.081

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.762
r_dihedral_angle_4_deg	17.229
r_dihedral_angle_3_deg	13.766
r_dihedral_angle_1_deg	6.544
r_angle_refined_deg	1.455
r_mcangle_it	1.195
r_angle_other_deg	1.104
r_mcbond_it	0.714
r_mcbond_other	0.714
r_chiral_restr	0.081
r_bond_refined_d	0.011
r_gen_planes_refined	0.007
r_bond_other_d	0.004
r_gen_planes_other	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13356
Nucleic Acid Atoms
Solvent Atoms	703
Heterogen Atoms	265

Software

Software
Software Name	Purpose
Aimless	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	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 R01GM133198.