5HKO | pdb_00005hko

Crystal structure of ABC transporter Solute Binding Protein MSMEG_3598 from Mycobacterium smegmatis str. MC2 155, target EFI-510969, in complex with L-sorbitol

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4RS3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	298	Protein (10 mM HEPES pH 7.5, 5 mM DTT, 10 mM L-sorbitol); Reservoir (MCSG4 A7)(0.2 M Zinc Acetate Dihydrate, 0.1 M Imidazole pH 8, 2.5 M Sodium Chloride); Cryoprotection (20% Diethylene Glycol, 80% Reservoir)

Crystal Properties
Matthews coefficient	Solvent content
1.98	37.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.947	α = 90
b = 62.94	β = 90
c = 73.153	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	RAYONIX MX225HE	MIRRORS	2015-10-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.9793	APS	31-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.2	50	99.9	0.091	0.098	0.037	8.8	7.1		91508

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	1.2	1.24	99.7		0.685	0.74	0.277	0.829		7	9021

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	4RS3	1.2	47.71	86963	4465	99.95	0.1568	0.1558	0.16	0.1779	0.18	RANDOM	14.242

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]
-0.15			-0.21		0.36

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.938
r_dihedral_angle_4_deg	12.529
r_dihedral_angle_3_deg	12.051
r_dihedral_angle_1_deg	6.534
r_angle_refined_deg	2.828
r_mcangle_it	1.833
r_mcbond_it	1.273
r_mcbond_other	1.242
r_angle_other_deg	1.21
r_chiral_restr	0.168

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.938
r_dihedral_angle_4_deg	12.529
r_dihedral_angle_3_deg	12.051
r_dihedral_angle_1_deg	6.534
r_angle_refined_deg	2.828
r_mcangle_it	1.833
r_mcbond_it	1.273
r_mcbond_other	1.242
r_angle_other_deg	1.21
r_chiral_restr	0.168
r_bond_refined_d	0.036
r_gen_planes_refined	0.015
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2308
Nucleic Acid Atoms
Solvent Atoms	287
Heterogen Atoms	73

Software

Software
Software Name	Purpose
HKL-3000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
MOLREP	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.