3B9J | pdb_00003b9j

Structure of Xanthine Oxidase with 2-hydroxy-6-methylpurine

X-RAY DIFFRACTION

---

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	batch	7	298	PEG 8000, DTT, pyrophosphate, phosphate, TRIS, pH 7.0, batch, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.42	49.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 133.187	α = 90
b = 73.794	β = 98.87
c = 146.498	γ = 90

Symmetry
Space Group	P 1 21 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	MAR CCD 165 mm		2007-05-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.9793	APS	31-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.3	144.34				120613	114520

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.3	2.36

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 (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	1FIQ	2.3	144.34	120613	114520	6093	96.25	0.197	0.194	0.2	0.263	0.27	RANDOM	22.698

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]
-2.04		1.13	-0.55		2.94

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.172
r_dihedral_angle_4_deg	19.786
r_dihedral_angle_3_deg	18.141
r_dihedral_angle_1_deg	9.919
r_scangle_it	2.888
r_scbond_it	1.878
r_angle_refined_deg	1.798
r_mcangle_it	1.228
r_angle_other_deg	1.078
r_mcbond_it	0.743
r_symmetry_vdw_refined	0.379
r_symmetry_hbond_refined	0.324
r_symmetry_vdw_other	0.297
r_xyhbond_nbd_refined	0.222
r_nbd_refined	0.22
r_nbd_other	0.212
r_nbtor_refined	0.178
r_chiral_restr	0.152
r_mcbond_other	0.143
r_nbtor_other	0.091
r_xyhbond_nbd_other	0.046
r_bond_refined_d	0.017
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	18785
Nucleic Acid Atoms
Solvent Atoms	861
Heterogen Atoms	201

Software

Software
Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
At	data scaling