5MEL

Structure of an E333Q variant of the GH99 endo-alpha-mannanase from Bacteroides xylanisolvens in complex with Glc-alpha-1,3-(3R,4R,5R)-5-(hydroxymethyl)cyclohex-1,2-ene-3,4-diol


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.42923M sodium acetate, pH 7.4
Crystal Properties
Matthews coefficientSolvent content
2.2846.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 108.791α = 90
b = 108.791β = 90
c = 67.85γ = 90
Symmetry
Space GroupI 4

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2014-10-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.92DiamondI04-1

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
11.239.5498.70.0590.99915.37.912191512.5
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)
11.21.2282.70.9550.5431.75.3

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 REPLACEMENTTHROUGHOUTmodified 4UTF1.239.54115855606098.640.119480.118530.13743RANDOM17.21
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]
-0.64-0.641.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.882
r_sphericity_free26.258
r_dihedral_angle_4_deg20.679
r_dihedral_angle_3_deg12.172
r_sphericity_bonded10.663
r_dihedral_angle_1_deg8.441
r_long_range_B_refined3.047
r_long_range_B_other2.85
r_scangle_other2.569
r_scbond_other2.122
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.882
r_sphericity_free26.258
r_dihedral_angle_4_deg20.679
r_dihedral_angle_3_deg12.172
r_sphericity_bonded10.663
r_dihedral_angle_1_deg8.441
r_long_range_B_refined3.047
r_long_range_B_other2.85
r_scangle_other2.569
r_scbond_other2.122
r_scbond_it2.121
r_mcangle_other1.981
r_mcangle_it1.976
r_rigid_bond_restr1.798
r_angle_refined_deg1.586
r_mcbond_it1.449
r_mcbond_other1.431
r_angle_other_deg1.059
r_chiral_restr0.098
r_bond_refined_d0.012
r_gen_planes_refined0.011
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 Atoms2799
Nucleic Acid Atoms
Solvent Atoms346
Heterogen Atoms29

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing