7OKZ | pdb_00007okz

CRYSTAL STRUCTURE OF THE COFACTOR-DEVOID 1-H-3-HYDROXY-4- OXOQUINALDINE 2,4-DIOXYGENASE (HOD) CATALYTICALLY INACTIVE H251A VARIANT COMPLEXED WITH 2-METHYL- QUINOLIN-4(1H)-ONE UNDER HYPEROXIC CONDITIONS

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7OJM

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
2.38	48.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 120.52	α = 90
b = 120.52	β = 90
c = 44.74	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	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	2.1	60.26	99.4	0.09	0.041	12.7	6.3		37761			28.1

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	2.1	2.16			0.758	0.487

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	7OJM	2.101	60.26	37749	1793	99.358	0.192	0.1902	0.19	0.2284	0.23	35.554

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]
0.72			0.72		-1.439

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.851
r_dihedral_angle_4_deg	16.592
r_dihedral_angle_3_deg	14.771
r_dihedral_angle_1_deg	6.449
r_lrange_it	5.821
r_lrange_other	5.733
r_scangle_it	3.865
r_scangle_other	3.865
r_mcangle_it	3.482
r_mcangle_other	3.482
r_scbond_it	2.637
r_scbond_other	2.637
r_mcbond_it	2.414
r_mcbond_other	2.413
r_angle_refined_deg	1.324
r_angle_other_deg	1.212
r_nbd_other	0.296
r_symmetry_nbd_refined	0.266
r_metal_ion_refined	0.236
r_xyhbond_nbd_refined	0.216
r_nbd_refined	0.198
r_symmetry_nbd_other	0.191
r_symmetry_xyhbond_nbd_refined	0.167
r_nbtor_refined	0.16
r_symmetry_nbtor_other	0.077
r_chiral_restr	0.064
r_ncsr_local_group_1	0.053
r_symmetry_xyhbond_nbd_other	0.043
r_bond_refined_d	0.006
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4461
Nucleic Acid Atoms
Solvent Atoms	255
Heterogen Atoms	54

Software

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