3K4U

CRYSTAL STRUCTURE OF putative binding component of ABC transporter from Wolinella succinogenes DSM 1740 complexed with lysine


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.529810% iso-propanol, 0.1 M Hepes, 20% PEG 4000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.7955.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.406α = 90
b = 149.151β = 100.46
c = 81.969γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152009-07-15SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29ANSLSX29A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.625099.30.12473.7100715
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.72.7592.33.1

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 DIFFRACTIONSADTHROUGHOUT2.622051195265790.60.2050.2020.266RANDOM32.41
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]
-5.47-6.33-4.149.61
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.276
r_dihedral_angle_4_deg25.341
r_dihedral_angle_3_deg23.314
r_scbond_it11.276
r_dihedral_angle_1_deg7.272
r_mcangle_it4.811
r_angle_refined_deg1.701
r_mcbond_it1.082
r_scangle_it1.033
r_chiral_restr0.122
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.276
r_dihedral_angle_4_deg25.341
r_dihedral_angle_3_deg23.314
r_scbond_it11.276
r_dihedral_angle_1_deg7.272
r_mcangle_it4.811
r_angle_refined_deg1.701
r_mcbond_it1.082
r_scangle_it1.033
r_chiral_restr0.122
r_bond_refined_d0.014
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11238
Nucleic Acid Atoms
Solvent Atoms116
Heterogen Atoms60

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
SHELXDphasing