6TEP | pdb_00006tep

Crystal structure of a galactokinase from Bifidobacterium infantis in complex with ADP

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1PIE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	0.1 M MES pH 6.0, 0.15 - 0.25 M NaCl and 18 - 22 % (w/v) polyethylene glycol 6000).

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.272	α = 90
b = 164.495	β = 95.8
c = 115.873	γ = 90

Symmetry
Space Group	P 1 21 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 6M		2017-12-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

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	1.45	94.58	98.4	0.095	7.3	4		336915

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	1.45	1.47	95.6		0.663

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	1PIE	1.45	94.58	319927	16932	98.26	0.1871	0.184	0.1891	0.2449	0.2483	RANDOM	17.661

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]
-0.41		-0.95	0.43		0.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.865
r_dihedral_angle_4_deg	17.29
r_dihedral_angle_3_deg	13.54
r_dihedral_angle_1_deg	6.918
r_rigid_bond_restr	4.836
r_angle_refined_deg	1.939
r_angle_other_deg	1.635
r_chiral_restr	0.107
r_bond_refined_d	0.016
r_gen_planes_refined	0.012

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.865
r_dihedral_angle_4_deg	17.29
r_dihedral_angle_3_deg	13.54
r_dihedral_angle_1_deg	6.918
r_rigid_bond_restr	4.836
r_angle_refined_deg	1.939
r_angle_other_deg	1.635
r_chiral_restr	0.107
r_bond_refined_d	0.016
r_gen_planes_refined	0.012
r_bond_other_d	0.005
r_gen_planes_other	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12295
Nucleic Acid Atoms
Solvent Atoms	1475
Heterogen Atoms	261

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
DIALS	data reduction
Aimless	data scaling
PHASER	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.