1JRP | pdb_00001jrp

Crystal Structure of Xanthine Dehydrogenase inhibited by alloxanthine from Rhodobacter capsulatus

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	295	PEG, Tris, DTT, isopropanol at pH 8.0, VAPOR DIFFUSION, HANGING DROP at 295K

Crystal Properties
Matthews coefficient	Solvent content
3.2	44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 92.617	α = 109.59
b = 140.728	β = 105.84
c = 157.665	γ = 101.25

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 QUANTUM 4		2001-04-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X4A	0.900	NSLS	X4A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	3	30	99.1	0.159	10.1	4.1	135608	135608		-1000

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3	3.1			0.741	2.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1JRO	3	30	-1000	128790	128790	6818	99.07	0.196	0.196	0.193	0.243	RANDOM	35.64

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]
1.7	-0.37	0.01	-2.65	-1.92	-0.47

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	5.078
r_scbond_it	3.094
r_angle_refined_deg	2.724
r_mcangle_it	1.871
r_mcbond_it	0.99
r_symmetry_hbond_refined	0.395
r_nbd_refined	0.219
r_xyhbond_nbd_refined	0.195
r_chiral_restr	0.151
r_bond_refined_d	0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	5.078
r_scbond_it	3.094
r_angle_refined_deg	2.724
r_mcangle_it	1.871
r_mcbond_it	0.99
r_symmetry_hbond_refined	0.395
r_nbd_refined	0.219
r_xyhbond_nbd_refined	0.195
r_chiral_restr	0.151
r_bond_refined_d	0.03
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	36348
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	400

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	model building
REFMAC	refinement
X-PLOR	phasing

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.