5JBE | pdb_00005jbe

4,6-alpha-glucanotransferase GTFB from Lactobacillus reuteri 121 complexed with an isomalto-maltopentasaccharide

X-RAY DIFFRACTION

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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)2)SO4

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 220.441	α = 90
b = 58.324	β = 114.25
c = 151.41	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		2014-10-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.8729	ESRF	ID23-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.1	46.16	99.4	0.126	0.145	0.071	0.994	7.7	4		102167

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	2.1	2.14	98.9		0.818		3.7

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ID: 3KLK domains A, B, C, IV	2.1	46.16	97017	5150	99.16	0.2079	0.2064	0.2124	0.2377	0.243	RANDOM	39.018

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]
0.55		1.01	-3.06		1.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.543
r_dihedral_angle_4_deg	16.192
r_dihedral_angle_3_deg	13.746
r_dihedral_angle_1_deg	6.069
r_angle_refined_deg	1.336
r_angle_other_deg	1.119
r_mcangle_it	0.897
r_mcbond_it	0.531
r_mcbond_other	0.52
r_chiral_restr	0.076
r_bond_refined_d	0.01
r_gen_planes_refined	0.005
r_bond_other_d	0.004
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13356
Nucleic Acid Atoms
Solvent Atoms	623
Heterogen Atoms	193

Software

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