5B0S

Beta-1,2-Mannobiose phosphorylase from Listeria innocua - beta-1,2-mannotriose complex


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.62931.8 M (NH4)2SO4, 10 mM CoCl2, 0.1 M MES-NaOH
Crystal Properties
Matthews coefficientSolvent content
4.0169.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 145.545α = 90
b = 145.545β = 90
c = 105.744γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102014-11-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW12A1.000Photon FactoryAR-NW12A

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
12.1501000.0729.88.375403
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)
12.12.141000.6892.87.2

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 REPLACEMENTTHROUGHOUT1VKD2.143.4471175378399.30.180950.179140.21491RANDOM39.357
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
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.473
r_dihedral_angle_4_deg16.622
r_dihedral_angle_3_deg13.499
r_dihedral_angle_1_deg7.392
r_long_range_B_refined7.353
r_long_range_B_other7.352
r_scangle_other6.137
r_scbond_it4.38
r_scbond_other4.379
r_mcangle_it4.051
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.473
r_dihedral_angle_4_deg16.622
r_dihedral_angle_3_deg13.499
r_dihedral_angle_1_deg7.392
r_long_range_B_refined7.353
r_long_range_B_other7.352
r_scangle_other6.137
r_scbond_it4.38
r_scbond_other4.379
r_mcangle_it4.051
r_mcangle_other4.051
r_mcbond_it3.358
r_mcbond_other3.357
r_angle_refined_deg2.076
r_angle_other_deg1.116
r_chiral_restr0.13
r_bond_refined_d0.035
r_bond_other_d0.011
r_gen_planes_refined0.011
r_gen_planes_other0.002
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 Atoms5639
Nucleic Acid Atoms
Solvent Atoms349
Heterogen Atoms161

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing