8OIW | pdb_00008oiw

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8OH8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	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 0.8M K/Na tartrate tetrahydrate, 0.1 M HEPES pH 7.5 using a 1:1 ratio. Crystals were 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
2.6	52.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 101.775	α = 90
b = 124.859	β = 90
c = 128.265	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 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	1.89	78.89	100	0.17	0.048	0.998	7.6	13.5		131041

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	1.89	1.92	98.1		0.405	0.123	0.253	0.3	11.4

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	1.89	78.888	128034	6233	97.677	0.189	0.1881	0.19	0.2145	0.22	41.869

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]
-0.517			-0.129		0.646

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.123
r_dihedral_angle_3_deg	15.352
r_dihedral_angle_4_deg	14.366
r_dihedral_angle_1_deg	7.238
r_lrange_it	4.774
r_lrange_other	4.773
r_scangle_it	2.722
r_scangle_other	2.722
r_mcangle_it	2
r_mcangle_other	2
r_scbond_it	1.718
r_scbond_other	1.718
r_angle_refined_deg	1.414
r_mcbond_it	1.259
r_mcbond_other	1.259
r_angle_other_deg	1.25
r_symmetry_xyhbond_nbd_refined	0.299
r_nbd_other	0.219
r_nbd_refined	0.194
r_symmetry_nbd_other	0.176
r_xyhbond_nbd_refined	0.174
r_nbtor_refined	0.163
r_symmetry_nbd_refined	0.142
r_symmetry_xyhbond_nbd_other	0.1
r_symmetry_nbtor_other	0.074
r_chiral_restr	0.067
r_ncsr_local_group_4	0.059
r_ncsr_local_group_1	0.055
r_ncsr_local_group_5	0.055
r_ncsr_local_group_3	0.052
r_ncsr_local_group_2	0.051
r_ncsr_local_group_6	0.047
r_bond_refined_d	0.008
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9620
Nucleic Acid Atoms
Solvent Atoms	597
Heterogen Atoms	118

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
DIALS	data scaling
PHASER	phasing