5MEH

Crystal structure of alpha-1,2-mannosidase from Caulobacter K31 strain in complex with 1-deoxymannojirimycin


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52920.1 M Bis-Tris pH 6.5, 0.2 M ammonium acetate, 22% (w/v) polyethylene glycol 3350
Crystal Properties
Matthews coefficientSolvent content
2.0539.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 145.371α = 90
b = 145.371β = 90
c = 50.838γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2015-11-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.92819DiamondI04-1

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
10.9547.1498.9117.24.3249654
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
10.950.97910.490.631.72.1

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 DIFFRACTIONTHROUGHOUT0.9547.142370361261898.830.09170.091090.1032RANDOM10.764
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]
0.170.080.17-0.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.337
r_sphericity_free29.977
r_dihedral_angle_4_deg17.623
r_dihedral_angle_3_deg12.07
r_sphericity_bonded10.146
r_dihedral_angle_1_deg6.417
r_rigid_bond_restr5.413
r_scangle_other4.633
r_scbond_it4.498
r_scbond_other4.497
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.337
r_sphericity_free29.977
r_dihedral_angle_4_deg17.623
r_dihedral_angle_3_deg12.07
r_sphericity_bonded10.146
r_dihedral_angle_1_deg6.417
r_rigid_bond_restr5.413
r_scangle_other4.633
r_scbond_it4.498
r_scbond_other4.497
r_long_range_B_other3.948
r_long_range_B_refined3.946
r_angle_refined_deg2.038
r_mcangle_other1.938
r_mcangle_it1.937
r_mcbond_it1.341
r_mcbond_other1.317
r_angle_other_deg1.086
r_chiral_restr0.119
r_bond_refined_d0.026
r_gen_planes_refined0.014
r_gen_planes_other0.003
r_bond_other_d0.002
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3472
Nucleic Acid Atoms
Solvent Atoms505
Heterogen Atoms30

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling