3PK4 | pdb_00003pk4

Urate oxidase under 3.2 MPa / 32 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-1 Urate oxidase; 2 mg.ml-1 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
2.99	58.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.405	α = 90
b = 96.311	β = 90
c = 105.593	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 315r	MIRRORS	2010-09-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM30A	0.9797	ESRF	BM30A

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	1.85	30	99.9	0.064	15.3	4.8		35288		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	1.85	1.95	99.9	99.9	0.31	5.1	4.8

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	1.85	19.76	33452	1766	99.75	0.16109	0.15936	0.16	0.19341	0.19	RANDOM	25.571

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]
			-0.02		0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.126
r_dihedral_angle_3_deg	12.715
r_dihedral_angle_4_deg	11.375
r_dihedral_angle_1_deg	6.038
r_scangle_it	4.546
r_scbond_it	2.675
r_mcangle_it	1.786
r_angle_refined_deg	1.546
r_mcbond_it	0.928
r_chiral_restr	0.107
r_bond_refined_d	0.015
r_gen_planes_refined	0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_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	163
Heterogen Atoms	14

Software

Software
Software Name	Purpose
ADSC	data collection
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling