8OIH | pdb_00008oih

Crystal structure of the cysteine-rich Gallus gallus urate oxidase in complex with the 8-azaxanthine inhibitor under oxidising conditions (space group C 2 2 21)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7OFK

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.8	291.15	His6-tagged GgUOX at approx. 22 mg/ml in 50 mM Tris-HCl pH 8.0, 10 mM NaCl, 1 mM TCEP-HCl was incubated with a 20-fold molar excess of AZA. Crystals were obtained by mixing the protein with 8% PGA-LM, 0.3M KBr, 0.1M Tris-HCl pH 7.8 using a 1:1 ratio. Crystals were then transferred into cryoprotective solutions supplemented with 100 mM H2O2 and devoid of the TCEP-HCl reducing agent for approximately 15 minutes prior to cryocooling in liquid nitrogen.

Crystal Properties
Matthews coefficient	Solvent content
2.57	52.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 106.51	α = 90
b = 125.99	β = 90
c = 240.68	γ = 90

Symmetry
Space Group	C 2 2 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 PILATUS3 6M		2021-09-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.97948	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	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	1.86	77.06	100	0.116	0.033	0.999	12.1	13.8		135367

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.86	1.89	100		0.403	0.11	0.3	0.5	14.2

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.86	77.058	135131	6736	99.858	0.174	0.1719	0.18	0.2064	0.21	45.567

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]
0.812			-1.637		0.825

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.14
r_dihedral_angle_3_deg	14.517
r_dihedral_angle_4_deg	13.776
r_dihedral_angle_1_deg	7.235
r_lrange_it	5.518
r_lrange_other	5.41
r_scangle_it	3.007
r_scangle_other	3.007
r_mcangle_it	2.026
r_mcangle_other	2.026
r_scbond_it	1.993
r_scbond_other	1.991
r_angle_refined_deg	1.483
r_mcbond_it	1.392
r_mcbond_other	1.39
r_angle_other_deg	1.28
r_nbd_refined	0.195
r_xyhbond_nbd_refined	0.193
r_symmetry_nbd_other	0.177
r_nbd_other	0.177
r_nbtor_refined	0.163
r_symmetry_xyhbond_nbd_refined	0.161
r_symmetry_nbd_refined	0.127
r_chiral_restr	0.075
r_symmetry_nbtor_other	0.075
r_symmetry_xyhbond_nbd_other	0.018
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9641
Nucleic Acid Atoms
Solvent Atoms	747
Heterogen Atoms	202

Software

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