8OH8 | pdb_00008oh8

Crystal structure of the cysteine-rich Gallus gallus urate oxidase in complex with the 8-azaxanthine inhibitor under reducing 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	7A0L

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

Crystal Properties
Matthews coefficient	Solvent content
2.56	51.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 102.22	α = 90
b = 124.4	β = 90
c = 125.77	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		2021-07-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.97950	Diamond	I24

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	2.12	66.88	100	0.186	0.07	0.997	8.1	8		91505

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	2.12	2.16	100		2.54	0.934	0.363	0.9	8.2

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	2.12	66.88	91421	4563	99.963	0.187	0.1854	0.19	0.2141	0.21	46.99

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]
1.57			-1.935		0.365

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.374
r_dihedral_angle_4_deg	15.7
r_dihedral_angle_3_deg	15.226
r_dihedral_angle_1_deg	7.574
r_lrange_it	5.123
r_lrange_other	5.09
r_scangle_it	3.251
r_scangle_other	3.25
r_mcangle_it	2.492
r_mcangle_other	2.492
r_scbond_it	2.091
r_scbond_other	2.087
r_mcbond_it	1.564
r_mcbond_other	1.564
r_angle_refined_deg	1.451
r_angle_other_deg	1.25
r_symmetry_xyhbond_nbd_refined	0.227
r_nbd_other	0.222
r_symmetry_nbd_refined	0.194
r_nbd_refined	0.191
r_symmetry_nbd_other	0.173
r_nbtor_refined	0.16
r_xyhbond_nbd_refined	0.152
r_symmetry_nbtor_other	0.073
r_chiral_restr	0.07
r_ncsr_local_group_2	0.063
r_ncsr_local_group_4	0.063
r_ncsr_local_group_1	0.06
r_ncsr_local_group_3	0.057
r_ncsr_local_group_6	0.055
r_ncsr_local_group_5	0.054
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	9602
Nucleic Acid Atoms
Solvent Atoms	434
Heterogen Atoms	162

Software

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