8J79 | pdb_00008j79

Bovine Xanthine Oxidoreductase Crystallized with oxypurinol

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1FO4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE		293	The enzyme solution was exchanged buffer into 50 mM Tris-HCl pH 7.4 and diluted with 50 mM Tris-HCl pH 7.4, 5 mM DTT, 100 micro M oxypurinol, and 30% glycerol to a concentration of 8.6 mg/ml. The precipitant solution contained 50 mM potassium phosphate pH 6.0, 5 mM DTT, 0.2 mM EDTA, 100 micro M oxypurinol, 30% glycerol and 14%-15% PEG 4000. 10 micro L enzyme solution and 10 micro L reservoir solution were mixed on siliconized glass plates and kept in the dark at 20 C for 5 days.

Crystal Properties
Matthews coefficient	Solvent content
2.73	54.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 167.678	α = 90
b = 123.47	β = 90.89
c = 150.059	γ = 90

Symmetry
Space Group	C 1 2 1

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 EIGER X 16M		2020-07-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44XU	0.9	SPring-8	BL44XU

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	1.99	48.43	99.7	0.996	10.6	5		210046

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	1.99	2.11			0.843

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.99	47.72	199435	10629	99.74	0.16515	0.16346	0.17	0.19667	0.2	RANDOM	29.898

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.823
r_dihedral_angle_4_deg	15.529
r_dihedral_angle_3_deg	13.276
r_dihedral_angle_1_deg	6.975
r_long_range_B_refined	5.806
r_long_range_B_other	5.697
r_scangle_other	4.54
r_scbond_it	3.095
r_scbond_other	3.095
r_mcangle_it	3.065
r_mcangle_other	3.065
r_mcbond_it	2.312
r_mcbond_other	2.312
r_angle_refined_deg	1.623
r_angle_other_deg	1.381
r_chiral_restr	0.079
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001
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 Atoms	Number
Protein Atoms	19980
Nucleic Acid Atoms
Solvent Atoms	1815
Heterogen Atoms	248

Software

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