2W3R

Crystal Structure of Xanthine Dehydrogenase (desulfo form) from Rhodobacter capsulatus in complex with hypoxanthine

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1JRO	PDB ENTRY 1JRO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8.3		7.5 MM BACL2, 8% PEG 8000, 100 MM TRIS-HCL PH 8.3, 25 MM DTT AND 3% ISOPROPANOL

Crystal Properties
Matthews coefficient	Solvent content
3.34	59.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 92.77	α = 109.33
b = 139.94	β = 106.15
c = 158.04	γ = 101.05

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	MARMOSAIC 225 mm CCD		2008-07-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2		ESRF	ID23-2

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	2.7	51.03	98.2	0.14	6.4	1.97		183839

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	2.7	2.72	97.7		0.86	0.84	1.97

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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1JRO	2.9	51.23	141476	7476	98.2	0.242	0.24	0.24	0.281	0.28	RANDOM	53.09

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]
1.29	0.48	-1.7	-0.3	-1.69	-2.87

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.616
r_dihedral_angle_4_deg	17.077
r_dihedral_angle_3_deg	16.407
r_dihedral_angle_1_deg	4.839
r_angle_refined_deg	0.983
r_scangle_it	0.772
r_scbond_it	0.457
r_mcangle_it	0.41
r_mcbond_it	0.219
r_chiral_restr	0.062
r_bond_refined_d	0.006
r_gen_planes_refined	0.003
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	81
Heterogen Atoms	400

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing