3PKL

Urate oxidase under 0.8 MPa / 8 bars pressure of xenon

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2IBA	PDB entry 2IBA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH	8.5	298	10-15 mg/ml Urate oxidase, 2 mg/ml 8-azaxanthine, 50 mM Tris/HCl pH 8.5, 5-8 % PEG 8000, 0-0.05 M NaCl, BATCH, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.98	58.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.276	α = 90
b = 96.327	β = 90
c = 105.495	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	298	CCD	ADSC QUANTUM 210r	MIRRORS	2008-07-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM16	0.979	ESRF	BM16

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.749	30	90.7	0.061	24.2	5.3		37664		1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.749	1.81	95.1		0.447	3	5.2

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	RIGID BODY	THROUGHOUT	PDB entry 2IBA	1.749	14.99	35747	1893	90.69	0.17409	0.17292	0.19586	RANDOM	24.714

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]
0.01			-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.703
r_dihedral_angle_3_deg	12.557
r_dihedral_angle_4_deg	8.905
r_dihedral_angle_1_deg	6.034
r_scangle_it	4.354
r_scbond_it	2.637
r_mcangle_it	1.766
r_angle_refined_deg	1.398
r_mcbond_it	0.947
r_nbtor_refined	0.31
r_nbd_refined	0.203
r_symmetry_vdw_refined	0.178
r_symmetry_hbond_refined	0.143
r_xyhbond_nbd_refined	0.136
r_chiral_restr	0.103
r_metal_ion_refined	0.054
r_bond_refined_d	0.013
r_gen_planes_refined	0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2362
Nucleic Acid Atoms
Solvent Atoms	153
Heterogen Atoms	13

Software

Software
Software Name	Purpose
HKL-2000	data collection
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling