5OCP

The periplasmic binding protein component of the arabinose ABC transporter from Shewanella sp. ANA-3 bound to alpha and beta-L-arabinofuranose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2VK2 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2910.2 M Ammonium Nitrate, pH 6.2, 20 % PEG 3,350
Crystal Properties
Matthews coefficientSolvent content
2.1242.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.917α = 90
b = 86.327β = 90
c = 87.282γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120PIXELDECTRIS PILATUS3 6M2017-05-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9795DiamondI03

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
11.743.641000.0820.0880.0320.9983.777.462122
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.7399.90.5970.6430.2370.9037.1

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 REPLACEMENTTHROUGHOUT2VK21.743.6458975308199.910.16870.16690.2043RANDOM23.716
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]
-1.161.91-0.74
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.66
r_dihedral_angle_4_deg24.631
r_dihedral_angle_3_deg13.611
r_dihedral_angle_1_deg6.18
r_angle_refined_deg2.034
r_angle_other_deg1.086
r_chiral_restr0.131
r_bond_refined_d0.02
r_gen_planes_refined0.01
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.66
r_dihedral_angle_4_deg24.631
r_dihedral_angle_3_deg13.611
r_dihedral_angle_1_deg6.18
r_angle_refined_deg2.034
r_angle_other_deg1.086
r_chiral_restr0.131
r_bond_refined_d0.02
r_gen_planes_refined0.01
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4618
Nucleic Acid Atoms
Solvent Atoms461
Heterogen Atoms92

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
MOLREPphasing