4RXM

Crystal structure of periplasmic ABC transporter solute binding protein A7JW62 from Mannheimia haemolytica PHL213, Target EFI-511105, in complex with Myo-inositol


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.2294PROTEIN (10 MM HEPES PH 7.5, 5 MM DTT, 10 MM MYOINOSITOL); RESERVOIR: 0.1 M Na2HPO4:Citric Acid, PH 4.2, 0.2 M SODIUM CHLORIDE, 20% PEG8000; CRYOPROTECTION: RESERVOIR SOLUTION PLUS 20% GLUCOSE (VOL/VOL); VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
2.7955.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.784α = 90
b = 120.175β = 90
c = 137.741γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HEMIRRORS2014-12-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 31-IDAPS31-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)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
11.755099.80.090.0933.314.868349-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.751.781000.970.973.514.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONSADTHROUGHOUT1.755068349214899.240.156610.155660.18733RANDOM35.649
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]
2.34-0.45-1.88
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.355
r_dihedral_angle_4_deg18.244
r_dihedral_angle_3_deg14.025
r_long_range_B_other10.966
r_long_range_B_refined10.955
r_scangle_other10.452
r_scbond_it8.67
r_scbond_other8.656
r_dihedral_angle_1_deg5.582
r_mcangle_other5.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.355
r_dihedral_angle_4_deg18.244
r_dihedral_angle_3_deg14.025
r_long_range_B_other10.966
r_long_range_B_refined10.955
r_scangle_other10.452
r_scbond_it8.67
r_scbond_other8.656
r_dihedral_angle_1_deg5.582
r_mcangle_other5.07
r_mcangle_it5.046
r_mcbond_it4.085
r_mcbond_other4.022
r_angle_refined_deg1.359
r_angle_other_deg0.78
r_chiral_restr0.082
r_bond_refined_d0.01
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4376
Nucleic Acid Atoms
Solvent Atoms470
Heterogen Atoms46

Software

Software
Software NamePurpose
SHELXmodel building
ARP/wARPmodel building
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
SHELXphasing