6XUT

Crystallographic structure of oligosaccharide dehydrogenase from Pycnoporus cinnabarinus, ligand-free form


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2942 M ammonium sulfate
Crystal Properties
Matthews coefficientSolvent content
2.3547.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.874α = 90
b = 61.592β = 90
c = 195.091γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2019-06-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I241DiamondI24

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.4397.7499.9114.512.7103248
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.431.570.791.72

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4YNT1.697.5510324874932388899.980.166260.164670.19648RANDOM39.759
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]
-4.344.140.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.941
r_dihedral_angle_1_deg15.713
r_dihedral_angle_4_deg15.521
r_dihedral_angle_3_deg15.412
r_long_range_B_refined7.223
r_long_range_B_other7.133
r_angle_refined_deg1.713
r_angle_other_deg1.425
r_scangle_other1.328
r_mcangle_other1.134
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.941
r_dihedral_angle_1_deg15.713
r_dihedral_angle_4_deg15.521
r_dihedral_angle_3_deg15.412
r_long_range_B_refined7.223
r_long_range_B_other7.133
r_angle_refined_deg1.713
r_angle_other_deg1.425
r_scangle_other1.328
r_mcangle_other1.134
r_mcangle_it1.133
r_scbond_it0.981
r_scbond_other0.858
r_mcbond_it0.697
r_mcbond_other0.696
r_chiral_restr0.086
r_bond_refined_d0.013
r_gen_planes_refined0.01
r_bond_other_d0.004
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 Atoms4399
Nucleic Acid Atoms
Solvent Atoms454
Heterogen Atoms196

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing