2PES | pdb_00002pes

Urate Oxidase in complex with tris-dipicolinate Lutetium

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	293	5% PEG 8000, 0.1 Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.95	58.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.55	α = 90
b = 95.32	β = 90
c = 104.33	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	CCD	MAR CCD 165 mm		2006-03-20	M	MAD
2	1
3	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM30A	0.979700, 1.341332	ESRF	BM30A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.518	47.673	96.6	0.066	0.066	4.7	6.6		59288			18

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.52	1.6	84.6		0.011	1.084	0.4	3.1	7489

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MAD	THROUGHOUT	1.6	15	51652	2605	98.42	0.18	0.179	0.19	0.195	0.21	RANDOM	18.887

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]
1.04			-0.48		-0.57

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.7
r_dihedral_angle_3_deg	13.297
r_sphericity_free	11.897
r_dihedral_angle_4_deg	8.793
r_dihedral_angle_1_deg	5.93
r_scangle_it	3.936
r_scbond_it	2.733
r_mcbond_it	1.783
r_mcangle_it	1.664
r_angle_refined_deg	1.358
r_angle_other_deg	0.809
r_mcbond_other	0.213
r_nbd_refined	0.2
r_nbd_other	0.2
r_nbtor_refined	0.181
r_symmetry_vdw_other	0.177
r_xyhbond_nbd_other	0.153
r_xyhbond_nbd_refined	0.152
r_symmetry_hbond_refined	0.14
r_nbtor_other	0.084
r_symmetry_vdw_refined	0.082
r_chiral_restr	0.08
r_bond_refined_d	0.011
r_bond_other_d	0.005
r_gen_planes_refined	0.005
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2360
Nucleic Acid Atoms
Solvent Atoms	234
Heterogen Atoms	86

Software

Software
Software Name	Purpose
SCALA	data scaling
SHARP	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction