Experiment: 3UNA

Crystal Structure of Bovine Milk Xanthine Dehydrogenase with NAD Bound

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1FO4	PDB Entry 1FO4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	Sitting Drop Batch Slide	7.5	293	12 mg/ml Xanthine Dehydrogenase (from Bovine Milk), 8 % Polyethylene Glycol 4000, 30 % Glycerol, 5 mM Dithiothreitol, 0.5 mM Sodium Salicylate, 0.2 m Ethylenediaminetetraacetic Acid, 16.65 mM Sodium Pyrophosphate (pH 8.5), 25 mM Potasium Phosphate (pH 6.5). , Sitting Drop Batch Slide, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.57	52.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 166.028	α = 90
b = 123.182	β = 91.02
c = 147.624	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	93	CCD	ADSC QUANTUM 4		1999-09-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-BM-D	0.99077	APS	14-BM-D

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	1.9	20	99.8	0.064	23.6	5.3	233141	232449	-3	-3

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	1.9	1.93	98.9		0.38	3.7	4.6	11481

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB Entry 1FO4	1.9	20	223526	221312	2214	96	0.181	0.1719	0.214	0.2013	Random

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]
0.5		-0.242	3.844		-4.344

RMS Deviations
Key	Refinement Restraint Deviation
c_angle_deg	1.3
c_bond_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	19998
Nucleic Acid Atoms
Solvent Atoms	1502
Heterogen Atoms	332

Software

Software
Software Name	Purpose
ADSC	data collection
EPMR	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling