5DVI

High resolution crystal Structure of glucose complexed periplasmic glucose binding protein (ppGBP) from P. putida CSV86


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.82950.1 M phosphate citrate buffer, 2 M ammonium sulphate
Crystal Properties
Matthews coefficientSolvent content
2.2745.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.94α = 90
b = 119.05β = 90
c = 66.6γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2014-07-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.9763ESRFBM14

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
11.2544.3999.716.416.24224933
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.251.3599.22.715.47

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.2540.762136081124599.680.123390.12190.15153RANDOM23.264
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]
0.95-0.89-0.07
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free35.352
r_dihedral_angle_2_deg34.255
r_dihedral_angle_4_deg22.164
r_sphericity_bonded17.349
r_dihedral_angle_3_deg11.744
r_dihedral_angle_1_deg5.667
r_long_range_B_refined5.464
r_long_range_B_other4.757
r_scangle_other4.228
r_scbond_it3.603
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free35.352
r_dihedral_angle_2_deg34.255
r_dihedral_angle_4_deg22.164
r_sphericity_bonded17.349
r_dihedral_angle_3_deg11.744
r_dihedral_angle_1_deg5.667
r_long_range_B_refined5.464
r_long_range_B_other4.757
r_scangle_other4.228
r_scbond_it3.603
r_scbond_other3.585
r_mcangle_other3.222
r_mcangle_it3.22
r_rigid_bond_restr3.184
r_mcbond_it2.737
r_mcbond_other2.721
r_angle_refined_deg1.599
r_angle_other_deg0.871
r_chiral_restr0.101
r_bond_refined_d0.012
r_gen_planes_refined0.009
r_bond_other_d0.002
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5952
Nucleic Acid Atoms
Solvent Atoms981
Heterogen Atoms87

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing