8WL7

X-ray structure of Enterobacter cloacae allose-binding protein in complex with D-allose


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.529310 mM D-allose, 200 mM ammonium sulfate, 25% (w/v) polyethylene glycol 3,350, 100 mM Bis-Tris
Crystal Properties
Matthews coefficientSolvent content
2.5852.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.23α = 90
b = 64.56β = 90
c = 89.99γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2022-03-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-5A1.0Photon FactoryBL-5A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
11.7448.9499.90.99925.26.535484
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.741.790.757

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 REPLACEMENTTHROUGHOUT1RPJ1.7448.9433702178299.90.171450.168380.23053RANDOM31.504
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]
0.060.1-0.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.296
r_dihedral_angle_4_deg15.434
r_dihedral_angle_3_deg15.132
r_scangle_other8.023
r_scbond_it7.565
r_scbond_other7.561
r_rigid_bond_restr7.394
r_dihedral_angle_1_deg7.297
r_mcangle_it5.103
r_mcbond_it4.546
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.296
r_dihedral_angle_4_deg15.434
r_dihedral_angle_3_deg15.132
r_scangle_other8.023
r_scbond_it7.565
r_scbond_other7.561
r_rigid_bond_restr7.394
r_dihedral_angle_1_deg7.297
r_mcangle_it5.103
r_mcbond_it4.546
r_mcbond_other4.46
r_angle_other_deg1.344
r_angle_refined_deg1.292
r_chiral_restr0.06
r_gen_planes_refined0.015
r_bond_refined_d0.007
r_gen_planes_other0.003
r_bond_other_d0.001
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_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2141
Nucleic Acid Atoms
Solvent Atoms161
Heterogen Atoms12

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing