3PKK | pdb_00003pkk

Urate oxidase under 0.5 MPa / 5 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	58.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.315	α = 90
b = 96.262	β = 90
c = 105.51	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	IMAGE PLATE	MAR scanner 345 mm plate	MIRRORS	2008-12-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14	1.0	ESRF	BM14

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	1.73	30	98.6	0.041	29.2	4.9		42090		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	1.73	1.79	94.2		0.259	4.2	4.1

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	PDB entry 2IBA	1.733	14.99	39905	2116	98.47	0.16453	0.16361	0.16	0.18175	0.18	RANDOM	20.481

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

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.444
r_dihedral_angle_3_deg	12.534
r_dihedral_angle_4_deg	7.595
r_dihedral_angle_1_deg	5.836
r_scangle_it	4.38
r_scbond_it	2.62
r_mcangle_it	1.74
r_angle_refined_deg	1.396
r_mcbond_it	0.906
r_nbtor_refined	0.309
r_nbd_refined	0.204
r_symmetry_vdw_refined	0.175
r_symmetry_hbond_refined	0.136
r_xyhbond_nbd_refined	0.117
r_chiral_restr	0.102
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_refined
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	186
Heterogen Atoms	13

Software

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