8OXN | pdb_00008oxn

CRYSTAL STRUCTURE OF THE COFACTOR-DEVOID 1-H-3-HYDROXY-4- OXOQUINALDINE 2,4-DIOXYGENASE (HOD) S101A VARIANT COMPLEXED WITH 2-METHYL-QUINOLIN-4(1H)-ONE UNDER NORMOXYC CONDITIONS

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2WJ4

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
2.37	48.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.8	α = 90
b = 167.79	β = 90
c = 167.91	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M-F		2015-02-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02	0.97949	Diamond	I02

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	46.56	99.8	0.092	0.04	12.7	7.1		86750

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	98.5		0.866	0.375	2.3

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	46.56	86659	4298	99.82	0.174	0.1734	0.18	0.1942	0.2	33.936

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]
-16.477			8.801		7.676

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.358
r_dihedral_angle_4_deg	18.281
r_dihedral_angle_3_deg	14.648
r_dihedral_angle_1_deg	6.615
r_lrange_it	5.625
r_lrange_other	5.624
r_scangle_it	4.077
r_scangle_other	4.077
r_mcangle_it	3.745
r_mcangle_other	3.745
r_scbond_it	2.8
r_scbond_other	2.8
r_mcbond_it	2.662
r_mcbond_other	2.661
r_angle_refined_deg	1.336
r_angle_other_deg	1.213
r_symmetry_nbd_refined	0.401
r_nbd_other	0.351
r_symmetry_xyhbond_nbd_refined	0.252
r_nbd_refined	0.193
r_symmetry_nbd_other	0.184
r_xyhbond_nbd_refined	0.174
r_nbtor_refined	0.162
r_symmetry_xyhbond_nbd_other	0.14
r_symmetry_nbtor_other	0.076
r_chiral_restr	0.067
r_ncsr_local_group_4	0.034
r_ncsr_local_group_6	0.033
r_ncsr_local_group_2	0.032
r_ncsr_local_group_3	0.032
r_ncsr_local_group_5	0.031
r_ncsr_local_group_1	0.027
r_bond_refined_d	0.006
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	8904
Nucleic Acid Atoms
Solvent Atoms	158
Heterogen Atoms	76

Software

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