7C6I | pdb_00007c6i

Crystal structure of beta-glycosides-binding protein (W177X) of ABC transporter in an open-liganded state bound to sophorose

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7C63

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH		293	0.2 M Ammonium sulphate, 50% PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
2.03	39.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.64	α = 90
b = 92.06	β = 112.85
c = 70.01	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	IMAGE PLATE	RIGAKU RAXIS IV++	VariMax HF	2018-12-28	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	1.7	54.9	99.8	0.092	0.103	0.046	0.993	11.1	4.7		80275

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	1.7	1.73	96.5		0.405	0.463	0.217	0.883		4.3

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	7C63	1.7	54.9	76206	4042	99.8	0.1677	0.1657	0.18	0.2073	0.21	RANDOM	21.936

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]
-11.23		-5.1	4		7.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.358
r_dihedral_angle_4_deg	16.057
r_dihedral_angle_3_deg	14.618
r_dihedral_angle_1_deg	6.408
r_angle_refined_deg	1.984
r_angle_other_deg	1.544
r_chiral_restr	0.109
r_bond_refined_d	0.014
r_gen_planes_refined	0.011
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.358
r_dihedral_angle_4_deg	16.057
r_dihedral_angle_3_deg	14.618
r_dihedral_angle_1_deg	6.408
r_angle_refined_deg	1.984
r_angle_other_deg	1.544
r_chiral_restr	0.109
r_bond_refined_d	0.014
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	6416
Nucleic Acid Atoms
Solvent Atoms	817
Heterogen Atoms	88

Software

Software
Software Name	Purpose
HKL-3000	data collection
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing
Coot	model building
REFMAC	refinement
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.