2W54

Crystal Structure of Xanthine Dehydrogenase from Rhodobacter capsulatus in Complex with Bound Inhibitor Pterin-6-aldehyde

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.3		100 MM TRIS PH 8.3, 6-8 % PEG 8000, 6-8 MM BACL, 5-25 MM DTT, 3-4 % ISOPROPANOL, 10-15 MG/ML PROTEIN, HANGING DROP VAPOR DIFFUSION

Crystal Properties
Matthews coefficient	Solvent content
3.35	63.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 92.571	α = 109.63
b = 140.695	β = 105.83
c = 157.859	γ = 101.23

Symmetry
Space Group	P 1

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	ADSC CCD	A DOUBLY FOCUSING TOROIDAL MIRROR		M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X26C		NSLS	X26C

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	3.3	50	99.1	0.18	8.9	4		102161

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	3.3	3.36	98.6		0.65	2.6	4

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1JRO	3.3	50	96884	5185	99.1	0.188	0.186	0.224	RANDOM	23.23

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]
1.22	-0.28	-0.5	-2.26	-1.87	-0.6

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.299
r_dihedral_angle_3_deg	16.858
r_dihedral_angle_4_deg	15.664
r_dihedral_angle_1_deg	4.79
r_angle_refined_deg	0.992
r_scangle_it	0.68
r_scbond_it	0.378
r_mcangle_it	0.204
r_mcbond_it	0.098
r_chiral_restr	0.064
r_bond_refined_d	0.006
r_gen_planes_refined	0.004
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	36372
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	416

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing