3PPQ

Structures of the substrate-binding protein provide insights into the multiple compatible solutes binding specificities of Bacillus subtilis ABC transporter OpuC


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1SW2 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.528928%(v/v) Polyethylene Glycol 400, 0.2M Calcium Chloride dihydrate, 0.1M HEPES-Na, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.2946.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.73α = 90
b = 90.15β = 90
c = 115.66γ = 90
Symmetry
Space GroupP 2 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2010-01-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U0.9701SSRFBL17U

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
11.95095.24952949529-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.9785.6

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1SW21.9136.3447018251197.940.22660.22570.2422RANDOM20.693
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]
-0.40.390.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.46
r_dihedral_angle_3_deg14.372
r_dihedral_angle_4_deg12.102
r_dihedral_angle_1_deg6.027
r_scangle_it3.643
r_scbond_it2.181
r_angle_refined_deg1.469
r_mcangle_it1.259
r_mcbond_it0.663
r_chiral_restr0.101
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.46
r_dihedral_angle_3_deg14.372
r_dihedral_angle_4_deg12.102
r_dihedral_angle_1_deg6.027
r_scangle_it3.643
r_scbond_it2.181
r_angle_refined_deg1.469
r_mcangle_it1.259
r_mcbond_it0.663
r_chiral_restr0.101
r_bond_refined_d0.017
r_gen_planes_refined0.012
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 Atoms4330
Nucleic Acid Atoms
Solvent Atoms123
Heterogen Atoms14

Software

Software
Software NamePurpose
MAR345dtbdata collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
SCALAdata scaling