5M7I

Crystal structure of GH125 1,6-alpha-mannosidase mutant from Clostridium perfringens in complex with 1,6-alpha-mannobiose


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7291200 mM MgCl2, 100 mM HEPES pH7.0, 27% polyethylene glycol 3350
Crystal Properties
Matthews coefficientSolvent content
2.2445

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.296α = 90
b = 43.734β = 96.87
c = 85.407γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2016-05-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.979DiamondI02

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
12.160.8691.60.164.62.924135
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)
12.12.1657.20.840.551.42.6

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 DIFFRACTIONTHROUGHOUT2.160.8622849122690.960.194520.191810.24698RANDOM27.622
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]
3.02-0.29-2.22-0.7
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.883
r_dihedral_angle_4_deg13.831
r_dihedral_angle_3_deg13.504
r_dihedral_angle_1_deg6.248
r_long_range_B_refined3.229
r_long_range_B_other3.229
r_scangle_other2.218
r_mcangle_it1.847
r_mcangle_other1.847
r_scbond_it1.356
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.883
r_dihedral_angle_4_deg13.831
r_dihedral_angle_3_deg13.504
r_dihedral_angle_1_deg6.248
r_long_range_B_refined3.229
r_long_range_B_other3.229
r_scangle_other2.218
r_mcangle_it1.847
r_mcangle_other1.847
r_scbond_it1.356
r_scbond_other1.356
r_angle_refined_deg1.284
r_mcbond_it1.164
r_mcbond_other1.163
r_angle_other_deg0.929
r_chiral_restr0.076
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3478
Nucleic Acid Atoms
Solvent Atoms125
Heterogen Atoms23

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling