5LQ4 | pdb_00005lq4

The Structure of ThcOx, the First Oxidase Protein from the Cyanobactin Pathways

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.75	293	1.0 M sodium citrate, 0.1 M CHES pH 7.75
2	VAPOR DIFFUSION	7.75	293	1.0 M sodium citrate, 0.1 M CHES pH 7.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 109.3	α = 90
b = 109.3	β = 90
c = 195.36	γ = 90

Symmetry
Space Group	P 41 21 2

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 PILATUS3 S 6M		2015-04-20	M	SINGLE WAVELENGTH
2	2	x-ray	50	PIXEL	DECTRIS PILATUS 12M		2016-02-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	1.7712	Diamond	I03
2	SYNCHROTRON	DIAMOND BEAMLINE I23	3.0955	Diamond	I23

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.65	72.84	100	0.083	17.9	8.1		35204			60.235

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.65	2.72	99.6		0.836	2.7	8.5

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.65	72.83	33383	1751	99.92	0.19815	0.19664	0.2	0.22838	0.22	RANDOM	74.681

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]
0.38			0.38		-0.75

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.047
r_dihedral_angle_4_deg	16.459
r_dihedral_angle_3_deg	13.562
r_long_range_B_refined	7.67
r_long_range_B_other	7.67
r_dihedral_angle_1_deg	6.711
r_scangle_other	5.199
r_mcangle_it	4.755
r_mcangle_other	4.755
r_scbond_it	3.218
r_scbond_other	3.217
r_mcbond_it	2.919
r_mcbond_other	2.919
r_angle_refined_deg	1.294
r_angle_other_deg	1.056
r_chiral_restr	0.071
r_bond_refined_d	0.008
r_gen_planes_refined	0.005
r_bond_other_d	0.003
r_gen_planes_other	0.003
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7344
Nucleic Acid Atoms
Solvent Atoms	4
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing