5HKO

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)
TypeSourceAccession CodeDetails
experimental modelPDB 4RS3 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8298Protein (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 coefficientSolvent content
1.9837.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.947α = 90
b = 62.94β = 90
c = 73.153γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HEMIRRORS2015-10-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 31-ID0.9793APS31-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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.25099.90.0910.0980.0378.87.191508
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)RedundancyNumber Unique Reflections (All)
11.21.2499.70.6850.740.2770.82979021

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4RS31.247.7186963446599.950.15680.15580.1779RANDOM14.242
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]
-0.15-0.210.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.938
r_dihedral_angle_4_deg12.529
r_dihedral_angle_3_deg12.051
r_dihedral_angle_1_deg6.534
r_angle_refined_deg2.828
r_mcangle_it1.833
r_mcbond_it1.273
r_mcbond_other1.242
r_angle_other_deg1.21
r_chiral_restr0.168
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.938
r_dihedral_angle_4_deg12.529
r_dihedral_angle_3_deg12.051
r_dihedral_angle_1_deg6.534
r_angle_refined_deg2.828
r_mcangle_it1.833
r_mcbond_it1.273
r_mcbond_other1.242
r_angle_other_deg1.21
r_chiral_restr0.168
r_bond_refined_d0.036
r_gen_planes_refined0.015
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2308
Nucleic Acid Atoms
Solvent Atoms287
Heterogen Atoms73

Software

Software
Software NamePurpose
HKL-3000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
MOLREPphasing