4R6K

Crystal structure of ABC transporter substrate-binding protein YesO from Bacillus subtilis, TARGET EFI-510761, an open conformation


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2DVU 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.5Protein: 10 mM BIS-TRIS, 500 mm NaCl, 5% glycerol, 5 mm DTT; reservoir: 1.4 m sodium citrate, 0.1 m HEPES-NaOH, pH 7.5; vapor diffusion, sitting drop, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
2.0941.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.932α = 90
b = 75.727β = 90
c = 119.738γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315MIRRORS2014-06-26MSINGLE 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)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
11.945099.30.0790.079256.930836-5
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)
11.941.9794.20.780.781.75.7

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 DIFFRACTIONMRTHROUGHOUT2DVU1.94502981995299.110.193830.19180.25981RANDOM39.652
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]
2.17-2.180.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.849
r_dihedral_angle_4_deg20.309
r_dihedral_angle_3_deg15.893
r_scangle_other13.727
r_long_range_B_other13.719
r_long_range_B_refined13.656
r_scbond_it13.434
r_scbond_other13.434
r_mcangle_other7.64
r_mcangle_it7.638
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.849
r_dihedral_angle_4_deg20.309
r_dihedral_angle_3_deg15.893
r_scangle_other13.727
r_long_range_B_other13.719
r_long_range_B_refined13.656
r_scbond_it13.434
r_scbond_other13.434
r_mcangle_other7.64
r_mcangle_it7.638
r_mcbond_it7.528
r_mcbond_other7.517
r_dihedral_angle_1_deg5.524
r_angle_refined_deg1.376
r_angle_other_deg0.791
r_chiral_restr0.088
r_bond_refined_d0.01
r_gen_planes_refined0.007
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 Atoms3179
Nucleic Acid Atoms
Solvent Atoms202
Heterogen Atoms1

Software

Software
Software NamePurpose
PHASERphasing
ARP/wARPmodel building
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling