6Z14

Structure of Bifidobacterium bifidum GH20 beta-N-beta-N-acetylhexosaminidase E553Q variant in complex with 4MU-6SGlcNAc-derived oxazoline


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6YXZ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.529321.6 MG/ML OF PURIFIED PROTEIN IN THE BUFFER OF TRIS 25 MM PH 8.0 AND NACL 200 MM IS MIXED WITH PEG 3350 21%, 0.1 M BIS-TRIS PROPANE PH 6.5 AND 0.2 M NANO3 AT 1:1
Crystal Properties
Matthews coefficientSolvent content
2.3848.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.423α = 90
b = 124.884β = 90
c = 151.682γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2020-03-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9795DiamondI04

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
11.6764.821000.1160.9967.47120710
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)
11.671.70.7320.75516.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE6YXZ1.6764.82120604603099.9380.1630.16040.205526.849
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]
1.842-0.959-0.883
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.727
r_dihedral_angle_4_deg16.402
r_dihedral_angle_3_deg13.251
r_dihedral_angle_1_deg7.166
r_lrange_it4.983
r_lrange_other4.734
r_scangle_it4.531
r_scangle_other4.53
r_mcangle_it3.675
r_mcangle_other3.675
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.727
r_dihedral_angle_4_deg16.402
r_dihedral_angle_3_deg13.251
r_dihedral_angle_1_deg7.166
r_lrange_it4.983
r_lrange_other4.734
r_scangle_it4.531
r_scangle_other4.53
r_mcangle_it3.675
r_mcangle_other3.675
r_scbond_it3.643
r_scbond_other3.643
r_mcbond_it2.956
r_mcbond_other2.954
r_rigid_bond_restr2.059
r_angle_refined_deg1.44
r_angle_other_deg1.39
r_nbd_other0.226
r_symmetry_nbd_refined0.218
r_nbd_refined0.202
r_symmetry_nbd_other0.183
r_nbtor_refined0.16
r_xyhbond_nbd_refined0.144
r_symmetry_xyhbond_nbd_refined0.142
r_metal_ion_refined0.111
r_symmetry_nbtor_other0.078
r_chiral_restr0.068
r_chiral_restr_other0.065
r_symmetry_xyhbond_nbd_other0.056
r_bond_refined_d0.008
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5264
Nucleic Acid Atoms
Solvent Atoms653
Heterogen Atoms43

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
MOLREPphasing