1JRO | pdb_00001jro

Crystal Structure of Xanthine Dehydrogenase from Rhodobacter capsulatus

X-RAY DIFFRACTION

Starting Model(s)

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

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 = 92.875	α = 109.53
b = 141.053	β = 105.83
c = 158.113	γ = 101.33

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		2001-02-14	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	CUSTOM-MADE		2001-03-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X26C	1.100	NSLS	X26C
2	SYNCHROTRON	NSLS BEAMLINE X25	1.100	NSLS	X25

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
1,2	2.7	50	99.2	0.17	11.2	3.8	187987	187987		-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)
1,2	2.7	2.8		98	0.73	2.7

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-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1FO4	2.7	50	178563	178563	9424	99.18	0.215	0.21505	0.21311	0.25154	RANDOM	39.67

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]
1.31	0.3	0.37	-1.57	-0.91	-0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	5.576
r_scbond_it	3.409
r_angle_refined_deg	2.346
r_mcangle_it	2.03
r_mcbond_it	1.068
r_symmetry_hbond_refined	0.291
r_nbd_refined	0.177
r_xyhbond_nbd_refined	0.177
r_chiral_restr	0.142
r_bond_refined_d	0.025

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	5.576
r_scbond_it	3.409
r_angle_refined_deg	2.346
r_mcangle_it	2.03
r_mcbond_it	1.068
r_symmetry_hbond_refined	0.291
r_nbd_refined	0.177
r_xyhbond_nbd_refined	0.177
r_chiral_restr	0.142
r_bond_refined_d	0.025
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	36348
Nucleic Acid Atoms
Solvent Atoms	123
Heterogen Atoms	360

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
REFMAC	refinement

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.