5L6F

Xylooligosaccharide oxidase from Myceliophthora thermophila C1 in complex with Xylobiose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5K8E 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP629415-18% PEG3350, 0.1 M MES buffer, 0.2 M ammonium chloride
Crystal Properties
Matthews coefficientSolvent content
2.346

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 123.591α = 90
b = 59.226β = 90.76
c = 68.502γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110IMAGE PLATEMARRESEARCH2015-09-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEBRUKER AXS MICROSTAR-H1.54

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.853.499.40.06611.43.64593111.3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.83900.2743.32.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT5K8E1.853.443668225299.380.153790.15230.18371RANDOM17.848
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]
0.2-0.30.14-0.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.806
r_dihedral_angle_4_deg15.047
r_dihedral_angle_3_deg11.484
r_dihedral_angle_1_deg6.914
r_long_range_B_refined4.932
r_long_range_B_other4.73
r_scangle_other2.206
r_angle_refined_deg1.454
r_scbond_it1.355
r_scbond_other1.354
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.806
r_dihedral_angle_4_deg15.047
r_dihedral_angle_3_deg11.484
r_dihedral_angle_1_deg6.914
r_long_range_B_refined4.932
r_long_range_B_other4.73
r_scangle_other2.206
r_angle_refined_deg1.454
r_scbond_it1.355
r_scbond_other1.354
r_mcangle_other1.191
r_mcangle_it1.19
r_angle_other_deg0.799
r_mcbond_it0.678
r_mcbond_other0.678
r_chiral_restr0.08
r_bond_refined_d0.01
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.001
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3673
Nucleic Acid Atoms
Solvent Atoms400
Heterogen Atoms234

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing