5H40

Crystal Structure of 1,2-beta-oligoglucan phosphorylase from Lachnoclostridium phytofermentans in complex with sophorose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5H3Z 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5298PEG3350, Tris-HCl, calcium acetate
Crystal Properties
Matthews coefficientSolvent content
2.4850.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86.78α = 90
b = 94.33β = 97.6
c = 156.92γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210r2014-12-21MSINGLE 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)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
12.286.0296.90.079.33.5123410
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)
12.22.2491.10.1364.33.55677

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 REPLACEMENTTHROUGHOUT5H3Z2.286.02117305610396.870.180980.179380.21139RANDOM27.695
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]
-0.01-0.010.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.27
r_dihedral_angle_4_deg18.695
r_dihedral_angle_3_deg14.33
r_dihedral_angle_1_deg6.867
r_long_range_B_refined5.376
r_long_range_B_other5.369
r_scangle_other4.176
r_mcangle_other3.164
r_mcangle_it3.163
r_scbond_it2.713
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.27
r_dihedral_angle_4_deg18.695
r_dihedral_angle_3_deg14.33
r_dihedral_angle_1_deg6.867
r_long_range_B_refined5.376
r_long_range_B_other5.369
r_scangle_other4.176
r_mcangle_other3.164
r_mcangle_it3.163
r_scbond_it2.713
r_scbond_other2.713
r_mcbond_it2.207
r_mcbond_other2.202
r_angle_refined_deg1.673
r_angle_other_deg1.325
r_chiral_restr0.102
r_bond_refined_d0.017
r_gen_planes_refined0.01
r_bond_other_d0.007
r_gen_planes_other0.005
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms17836
Nucleic Acid Atoms
Solvent Atoms743
Heterogen Atoms90

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
iMOSFLMdata scaling
MOLREPphasing