4N9M | pdb_00004n9m

Joint neutron/x-ray structure of urate oxidase in complex with 8-hydroxyxanthine

NEUTRON DIFFRACTION - X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	temperature-controlled batch	8.5	291	5 % PEG 8000, 0.1 M NACL, 0.1 M TRISHCL PD 8.5, 8 MG/ML URATE OXIDASE, temperature-controlled batch, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.98	58.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.18	α = 90
b = 96.26	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	293	IMAGE PLATE	MAR scanner 345 mm plate	Xenocs	2008-10-28	M	SINGLE WAVELENGTH
2	1	neutron	293	IMAGE PLATE	CUSTOM-MADE		2008-08-30	L	LAUE

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SEALED TUBE	OTHER	1.54
2	NUCLEAR REACTOR	OTHER	3.25-4.15

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	R Split (All)	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	2	20	98.5	0.04						23.56
2	2.3	40.06	72.2	0.133						7.9		13179	13179

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	R Split (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.14		0.145						9.54
2	2.3	2.42		0.19						2.2		1328

Refinement

Statistics
Diffraction ID	Structure Solution Method	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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		2.023	19.209		1.99		26344	1317	97.64		0.1678	0.1666	0.1647	0.1887	0.1842		19.13
NEUTRON DIFFRACTION		2.298	40.067				13174	663	71.08		0.2601	0.2586		0.2884

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]
15.7423			5.5013		1.3615
14.5584			7.9063		6.4684

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	16.275
f_angle_d	2.409
f_bond_d	0.075
f_chiral_restr	0.048
f_plane_restr	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2328
Nucleic Acid Atoms
Solvent Atoms	187
Heterogen Atoms	14

Software

Software
Software Name	Purpose
LADI-III	data collection
MOLREP	phasing
PHENIX	refinement
LAUEGEN	data reduction
SCALA	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.