2HPH

High resolution structure of E. coli glucose/galactose binding protein bound with glucose


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529020% PEG6000, 50mM NaHEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
2.0239.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.26α = 90
b = 36.58β = 107.19
c = 64.94γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2003-06-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID0.90APS22-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.332598.30.1615.226256662566-314.341
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.331.594.989.20.3433.1818133

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2GBP1.3324.57625666256431291000.1550.1550.1540.178RANDOM6.717
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]
-0.010.120.44-0.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.852
r_dihedral_angle_3_deg11.546
r_dihedral_angle_4_deg10.104
r_dihedral_angle_1_deg5.468
r_sphericity_free4.482
r_scangle_it3.059
r_scbond_it2.185
r_sphericity_bonded1.984
r_mcangle_it1.437
r_angle_refined_deg1.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.852
r_dihedral_angle_3_deg11.546
r_dihedral_angle_4_deg10.104
r_dihedral_angle_1_deg5.468
r_sphericity_free4.482
r_scangle_it3.059
r_scbond_it2.185
r_sphericity_bonded1.984
r_mcangle_it1.437
r_angle_refined_deg1.3
r_mcbond_it1.083
r_rigid_bond_restr1.001
r_angle_other_deg0.881
r_mcbond_other0.385
r_symmetry_vdw_refined0.286
r_nbd_refined0.225
r_nbd_other0.18
r_nbtor_refined0.175
r_symmetry_vdw_other0.169
r_xyhbond_nbd_refined0.122
r_symmetry_hbond_refined0.113
r_nbtor_other0.085
r_chiral_restr0.083
r_metal_ion_refined0.08
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2388
Nucleic Acid Atoms
Solvent Atoms523
Heterogen Atoms13

Software

Software
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
AMoREphasing