8PX9

Structure of the antibacterial peptide ABC transporter McjD, solved at wavelength 2.75 A


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29310% PEG 4000, 0.1 M ammonium sulphate, 100 mM HEPES pH 7.5 and 22% glycerol
Crystal Properties
Matthews coefficientSolvent content
3.9568.89

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.19α = 90
b = 109.32β = 90
c = 233.35γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray80PIXELDECTRIS PILATUS 12M2017-05-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I232.7552DiamondI23

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.854.6796.80.21460.21670.029650.99812.4854.65187383.08
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.82.90.6750.27

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 DIFFRACTIONSADTHROUGHOUT2.854.6749306257899.740.294060.292090.32974RANDOM163.335
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]
4.683.23-7.91
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined18.144
r_long_range_B_other18.144
r_dihedral_angle_3_deg15.242
r_scangle_other12.361
r_mcangle_it11.399
r_mcangle_other11.399
r_scbond_it7.844
r_scbond_other7.843
r_mcbond_it7.555
r_mcbond_other7.555
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined18.144
r_long_range_B_other18.144
r_dihedral_angle_3_deg15.242
r_scangle_other12.361
r_mcangle_it11.399
r_mcangle_other11.399
r_scbond_it7.844
r_scbond_other7.843
r_mcbond_it7.555
r_mcbond_other7.555
r_dihedral_angle_2_deg5.145
r_dihedral_angle_1_deg3.392
r_angle_refined_deg1.547
r_angle_other_deg0.789
r_chiral_restr0.082
r_bond_refined_d0.008
r_gen_planes_refined0.008
r_bond_other_d0.005
r_gen_planes_other0.005
r_dihedral_angle_4_deg
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 Atoms8913
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms64

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
HKL2Mapphasing