5LYR

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.8292.153 M sodium acetate, pH 6.8
Crystal Properties
Matthews coefficientSolvent content
2.2745.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 108.513α = 90
b = 108.513β = 90
c = 67.607γ = 90
Symmetry
Space GroupI 4

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2015-10-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.969DiamondI24

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
11.1476.7394.60.0510.99910.65.613477113.2
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)
11.141.1661.51.1580.3870.72.3

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 REPLACEMENTTHROUGHOUT4UTF1.1476.73127995670894.490.124730.123750.14333RANDOM18.123
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]
-0.29-0.290.58
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.131
r_sphericity_free30.305
r_dihedral_angle_4_deg19.351
r_dihedral_angle_3_deg12.441
r_dihedral_angle_1_deg8.871
r_sphericity_bonded8.375
r_long_range_B_refined3.202
r_long_range_B_other2.718
r_scangle_other1.973
r_scbond_it1.61
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.131
r_sphericity_free30.305
r_dihedral_angle_4_deg19.351
r_dihedral_angle_3_deg12.441
r_dihedral_angle_1_deg8.871
r_sphericity_bonded8.375
r_long_range_B_refined3.202
r_long_range_B_other2.718
r_scangle_other1.973
r_scbond_it1.61
r_scbond_other1.609
r_mcangle_other1.548
r_mcangle_it1.547
r_angle_refined_deg1.502
r_rigid_bond_restr1.463
r_mcbond_it1.165
r_mcbond_other1.141
r_angle_other_deg1.057
r_chiral_restr0.098
r_bond_refined_d0.011
r_gen_planes_refined0.01
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 Atoms2814
Nucleic Acid Atoms
Solvent Atoms422
Heterogen Atoms30

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
REFMACphasing