6JAD

Crystal structure of ABC transporter alpha-glycoside-binding protein in complex with palatinose

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6J9W

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	5	277	0.05 M Citric Acid, 0.05 M Bis-Tris Propane, 16% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.87	57.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.77	α = 90
b = 84.77	β = 90
c = 145.83	γ = 90

Symmetry
Space Group	P 41 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	IMAGE PLATE	RIGAKU RAXIS IV++	VariMax HF	2018-02-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

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	1.9	73.29	99.9	0.083	0.097	0.05	0.997	13.2	6.6		42666

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	9.11	99.6		0.449	0.524	0.268	0.915	3.6	6.9

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	6J9W	1.9	73.29	40512	2097	99.9	0.1415	0.1394	0.1816	RANDOM	22.409

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]
0.84			0.84		-1.68

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.738
r_dihedral_angle_4_deg	15.486
r_dihedral_angle_3_deg	13.363
r_dihedral_angle_1_deg	5.852
r_angle_refined_deg	1.804
r_angle_other_deg	0.902
r_chiral_restr	0.116
r_bond_refined_d	0.018
r_gen_planes_refined	0.011
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.738
r_dihedral_angle_4_deg	15.486
r_dihedral_angle_3_deg	13.363
r_dihedral_angle_1_deg	5.852
r_angle_refined_deg	1.804
r_angle_other_deg	0.902
r_chiral_restr	0.116
r_bond_refined_d	0.018
r_gen_planes_refined	0.011
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3227
Nucleic Acid Atoms
Solvent Atoms	517
Heterogen Atoms	49

Software

Software
Software Name	Purpose
HKL-3000	data collection
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing
REFMAC	refinement
Coot	model building
PDB_EXTRACT	data extraction

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.