4ND9

The putative substrate binding domain of ABC-type transporter from Agrobacterium tumefaciens in open conformation


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.2293PEG8000 20%, NaCl 0.2M, phosphate-citrate, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.4249.21

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.702α = 90
b = 64.155β = 90
c = 101.123γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rMIRROR2010-03-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97929APS19-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.35085.512333
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.3488.1

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 DIFFRACTIONSADTHROUGHOUT2.3501165859789.010.20220.199630.25282RANDOM22.94
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]
2.99-2.55-0.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.725
r_dihedral_angle_4_deg17.29
r_dihedral_angle_3_deg14.386
r_dihedral_angle_1_deg5.057
r_scangle_it1.847
r_scbond_it1.119
r_angle_refined_deg0.961
r_angle_other_deg0.822
r_mcangle_it0.636
r_mcbond_it0.326
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.725
r_dihedral_angle_4_deg17.29
r_dihedral_angle_3_deg14.386
r_dihedral_angle_1_deg5.057
r_scangle_it1.847
r_scbond_it1.119
r_angle_refined_deg0.961
r_angle_other_deg0.822
r_mcangle_it0.636
r_mcbond_it0.326
r_mcbond_other0.05
r_chiral_restr0.049
r_bond_refined_d0.007
r_gen_planes_refined0.003
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2070
Nucleic Acid Atoms
Solvent Atoms111
Heterogen Atoms

Software

Software
Software NamePurpose
HKL-3000data collection
SHELXSphasing
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling