8OXT | pdb_00008oxt

CRYSTAL STRUCTURE OF THE COFACTOR-DEVOID 1-H-3-HYDROXY-4- OXOQUINALDINE 2,4-DIOXYGENASE (HOD) H251A VARIANT COMPLEXED WITH N-ACETYLANTHRANILATE AS RESULT OF IN CRYSTALLO TURNOVER OF ITS NATURAL SUBSTRATE 1-H-3-HYDROXY-4- OXOQUINALDINE UNDER HYPEROXIC CONDITIONS

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2WJ3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7	293	PROTEIN AT 150 MG/ML IN STORAGE BUFFER 1.65M NA/K TARTRATE, 0.1M HEPES PH 7.0

Crystal Properties
Matthews coefficient	Solvent content
2.41	49.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 120.06	α = 90
b = 120.06	β = 90
c = 44.5	γ = 90

Symmetry
Space Group	P 41

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 315r		2014-11-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM30A	0.97981	ESRF	BM30A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	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	29.12	97.9	0.074	0.033	20.1	6.9		42489

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.05	89.9		0.639	0.535	1.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.003	29.12	37765	1910	87.421	0.205	0.203	0.21	0.2355	0.24	26.706

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]
0.683			0.683		-1.365

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.939
r_dihedral_angle_3_deg	16.855
r_dihedral_angle_4_deg	16.759
r_dihedral_angle_1_deg	6.961
r_lrange_it	4.657
r_lrange_other	4.599
r_scangle_it	2.708
r_scangle_other	2.708
r_mcangle_it	2.703
r_mcangle_other	2.701
r_mcbond_it	1.863
r_mcbond_other	1.862
r_scbond_it	1.825
r_scbond_other	1.825
r_angle_refined_deg	1.387
r_angle_other_deg	1.203
r_symmetry_nbd_refined	0.438
r_nbd_other	0.428
r_nbd_refined	0.223
r_symmetry_xyhbond_nbd_refined	0.212
r_symmetry_nbd_other	0.191
r_xyhbond_nbd_refined	0.188
r_metal_ion_refined	0.175
r_nbtor_refined	0.162
r_symmetry_nbtor_other	0.076
r_chiral_restr	0.066
r_ncsr_local_group_1	0.045
r_bond_refined_d	0.007
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	4440
Nucleic Acid Atoms
Solvent Atoms	167
Heterogen Atoms	82

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing