6HMG

Structure of the GH99 endo-alpha-mannanase from Bacteroides xylanisolvens in complex with alpha-Glc-1,3-(1,2-anhydro-carba-glucosamine)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5M17 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72923 M sodium acetate pH 7.0
Crystal Properties
Matthews coefficientSolvent content
2.2846.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 108.772α = 90
b = 108.772β = 90
c = 67.703γ = 90
Symmetry
Space GroupI 4

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-08-06MSINGLE 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)Rrim I (All)Rpim I (All)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
11.2739.51000.0580.0630.0240.99913.16.610377314
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.271.291001.2951.4090.550.5151.46.4

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 REPLACEMENTTHROUGHOUT5M171.2739.598601517299.930.133420.132320.15413RANDOM18.208
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]
-0.84-0.841.69
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.822
r_sphericity_free23.555
r_dihedral_angle_4_deg16.892
r_sphericity_bonded13.646
r_dihedral_angle_3_deg12.339
r_dihedral_angle_1_deg8.845
r_long_range_B_refined2.792
r_long_range_B_other2.631
r_scangle_other2.241
r_scbond_it1.959
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.822
r_sphericity_free23.555
r_dihedral_angle_4_deg16.892
r_sphericity_bonded13.646
r_dihedral_angle_3_deg12.339
r_dihedral_angle_1_deg8.845
r_long_range_B_refined2.792
r_long_range_B_other2.631
r_scangle_other2.241
r_scbond_it1.959
r_scbond_other1.956
r_mcangle_it1.826
r_mcangle_other1.826
r_rigid_bond_restr1.774
r_angle_refined_deg1.585
r_angle_other_deg1.515
r_mcbond_it1.435
r_mcbond_other1.434
r_chiral_restr0.092
r_gen_planes_refined0.01
r_bond_refined_d0.009
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms2809
Nucleic Acid Atoms
Solvent Atoms342
Heterogen Atoms26

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing