4AD2

Structure of the GH99 endo-alpha-mannosidase from Bacteroides xylanisolvens in complex with glucose-1,3-isofagomine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherPREVIOUSLY SOLVED STRUCTURE OF CLOSELY RELATED HOMOLOG

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.50.1 M SODIUM ACETATE PH 4.9, 20% W/V PEG 2000 MME, 1.6% PGA-LM (POLY-GAMMA-GLUTAMIC ACID LOW MOLECULAR WEIGHT)
Crystal Properties
Matthews coefficientSolvent content
3.5565.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 223.296α = 90
b = 223.296β = 90
c = 84.765γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MMIRRORS2011-05-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I03DiamondI03

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
12.1501000.1813.410.1140911224.5
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)
12.12.211000.873.610

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 REPLACEMENTTHROUGHOUTPREVIOUSLY SOLVED STRUCTURE OF CLOSELY RELATED HOMOLOG2.144.36133778704399.950.187610.186070.21674RANDOM28.882
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]
0.150.070.15-0.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.816
r_dihedral_angle_4_deg16.903
r_dihedral_angle_3_deg14.847
r_dihedral_angle_1_deg6.146
r_angle_refined_deg1.301
r_mcangle_it1.301
r_nbtor_refined0.314
r_nbd_refined0.206
r_symmetry_vdw_refined0.195
r_symmetry_hbond_refined0.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.816
r_dihedral_angle_4_deg16.903
r_dihedral_angle_3_deg14.847
r_dihedral_angle_1_deg6.146
r_angle_refined_deg1.301
r_mcangle_it1.301
r_nbtor_refined0.314
r_nbd_refined0.206
r_symmetry_vdw_refined0.195
r_symmetry_hbond_refined0.18
r_xyhbond_nbd_refined0.15
r_chiral_restr0.1
r_bond_refined_d0.013
r_mcbond_it0.013
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10953
Nucleic Acid Atoms
Solvent Atoms1374
Heterogen Atoms84

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing