4CW2 | pdb_00004cw2

Crystal structure of cofactor-free urate oxidase in complex with the 5-peroxo derivative of 9-metyl uric acid (X-ray dose, 2.5 kGy)

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8		20MG/ML UOX IN 50 MM TRIS-ACETATE PH 8.0 SATURATED WITH 9-METHYL URIC ACID UNDER ANAEROBIC CONDITIONS RESERVOIR: 8% PEG 8000, 50 MM TRIS-ACETATE PH 8.0 CRYSTALLIZATION WAS CARRIED OUT ANAEROBICALLY. CRYSTALS WERE EXPOSED TO AIR TO GENERATE THE PEROXIDE

Crystal Properties
Matthews coefficient	Solvent content
2.9	57.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.506	α = 90
b = 95.132	β = 90
c = 104.31	γ = 90

Symmetry
Space Group	I 2 2 2

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	MIRRORS	2013-07-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29		ESRF	ID29

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.32	50	100	0.11	8.8	6.6		92669		-1	10.82

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.32	1.37	99.9		0.72	2	6.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	OTHER	THROUGHOUT	NONE	1.32	70.29	88023	4635	99.93	0.11178	0.11044	0.127	0.13696	0.1477	RANDOM	15.409

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]
-1.01			0.71		0.31

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	60.78
r_sphericity_bonded	16.317
r_long_range_B_refined	7.766
r_long_range_B_other	5.439
r_scangle_other	3.503
r_rigid_bond_restr	3.131
r_mcangle_it	3.037
r_mcangle_other	3.037
r_mcbond_it	2.682
r_mcbond_other	2.681
r_scbond_it	2.661
r_scbond_other	2.66
r_angle_refined_deg	1.64
r_angle_other_deg	0.855
r_chiral_restr	0.098
r_bond_refined_d	0.013
r_gen_planes_refined	0.01
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_dihedral_angle_1_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
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

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2409
Nucleic Acid Atoms
Solvent Atoms	625
Heterogen Atoms	23

Software

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