5M03

Structure of the GH99 endo-alpha-mannanase from Bacteroides xylanisolvens in complex with mannose-alpha-1,3-noeuromycin and 1,2-alpha-mannobiose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4UTFmodified 4UTF

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.22923 M sodium acetate, pH 7.2
Crystal Properties
Matthews coefficientSolvent content
2.2445.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 108.033α = 90
b = 108.033β = 90
c = 67.45γ = 90
Symmetry
Space GroupI 4

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-10-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.979DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.0557.2199.30.0540.99910.85.917897411.87
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)
11.051.0789.11.3140.3080.72.7

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 REPLACEMENTTHROUGHOUTmodified 4UTF1.0557.21170072887299.30.115810.114880.13339RANDOM16.677
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]
0.250.25-0.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.32
r_sphericity_free35.197
r_dihedral_angle_4_deg18.249
r_dihedral_angle_3_deg12.123
r_sphericity_bonded10.291
r_dihedral_angle_1_deg8.712
r_long_range_B_refined3.72
r_long_range_B_other3.183
r_rigid_bond_restr2.387
r_scangle_other1.985
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.32
r_sphericity_free35.197
r_dihedral_angle_4_deg18.249
r_dihedral_angle_3_deg12.123
r_sphericity_bonded10.291
r_dihedral_angle_1_deg8.712
r_long_range_B_refined3.72
r_long_range_B_other3.183
r_rigid_bond_restr2.387
r_scangle_other1.985
r_scbond_it1.75
r_scbond_other1.75
r_angle_refined_deg1.673
r_mcangle_it1.634
r_mcangle_other1.634
r_mcbond_it1.236
r_mcbond_other1.235
r_angle_other_deg1.157
r_chiral_restr0.108
r_bond_refined_d0.013
r_gen_planes_refined0.012
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 Atoms2813
Nucleic Acid Atoms
Solvent Atoms468
Heterogen Atoms49

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
REFMACphasing