2ZKB | pdb_00002zkb

Urate oxidase complexed with 8-azaxanthine under 2.5 MPa oxygen pressure

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	298	10 mg/ml urate oxidase, 0.2mg/ml 8-azaxanthine, 50mM Tris, 20mM NaCl, PEG 8000 4-10%, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.96	58.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.753	α = 90
b = 96.285	β = 90
c = 105.427	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	277	CCD	MARMOSAIC 225 mm CCD	mirrors	2005-11-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14	0.97625	ESRF	BM14

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	1.61	50	98.8	0.055	10.9	3.4	52825	52204	1	1	19.5

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)
	1.61	1.67	97.6		0.374	2.15	3	5133

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	rigid body	THROUGHOUT	2IBA	1.61	14.96	49475	2658	98.79	0.17622	0.17519	0.18	0.19509	0.2	RANDOM	21.718

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.75
r_dihedral_angle_3_deg	13.154
r_dihedral_angle_4_deg	7.6
r_dihedral_angle_1_deg	5.971
r_scangle_it	4.056
r_scbond_it	2.461
r_mcangle_it	1.64
r_angle_refined_deg	1.493
r_mcbond_it	0.87
r_nbtor_refined	0.309
r_nbd_refined	0.212
r_symmetry_vdw_refined	0.169
r_symmetry_hbond_refined	0.137
r_xyhbond_nbd_refined	0.108
r_chiral_restr	0.102
r_metal_ion_refined	0.083
r_bond_refined_d	0.012
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	2379
Nucleic Acid Atoms
Solvent Atoms	192
Heterogen Atoms	17

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345dtb	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
REFMAC	phasing