6XUU

Crystallographic structure of oligosaccharide dehydrogenase from Pycnoporus cinnabarinus, glucose-bound form

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		294	2 M ammonium sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.137	α = 90
b = 61.618	β = 90
c = 195.954	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M		2019-11-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 11.2C	1.0	ELETTRA	11.2C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.57	49.04	99.6	0.99	12	6.6		103996

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.57	1.67			0.56

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	1.57	49.04	79572	4200	99.49	0.16358	0.16221	0.18889	RANDOM	34.753

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]
-3.38			3.25		0.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.393
r_dihedral_angle_1_deg	20.238
r_dihedral_angle_4_deg	17.636
r_dihedral_angle_3_deg	15.795
r_long_range_B_refined	5.791
r_long_range_B_other	5.724
r_angle_refined_deg	1.856
r_scangle_other	1.66
r_angle_other_deg	1.438
r_scbond_it	1.311
r_mcangle_other	1.259
r_mcangle_it	1.257
r_scbond_other	1.102
r_mcbond_it	0.8
r_mcbond_other	0.783
r_chiral_restr	0.093
r_bond_refined_d	0.013
r_gen_planes_refined	0.01
r_bond_other_d	0.003
r_gen_planes_other	0.002
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4399
Nucleic Acid Atoms
Solvent Atoms	354
Heterogen Atoms	251

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
REFMAC	phasing