6K8O

Crystal structure of the Sulfolobus solfataricus topoisomerase III in complex with DNA

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.6	293	0.1 M HEPES (pH 6.6), 2.25 M ammonium sulfate

Crystal Properties
Matthews coefficient	Solvent content
3.48	64.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 150.731	α = 90
b = 150.731	β = 90
c = 97.032	γ = 90

Symmetry
Space Group	P 42 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 PILATUS 2M		2015-12-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	1.0	Photon Factory	BL-5A

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	2.5	50	99.9	0.065	21.7	7.6		39128			50.8

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	2.5	2.54	99.9		0.882	1.9	7.1

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	FREE R-VALUE	2.5	50	37280	1939	99.92	0.22197	0.22008	0.259	RANDOM	49.085

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]
2.16			2.16		-4.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.004
r_dihedral_angle_4_deg	18.53
r_dihedral_angle_3_deg	15.324
r_dihedral_angle_1_deg	8.908
r_long_range_B_refined	7.251
r_long_range_B_other	7.218
r_scangle_other	6.689
r_scbond_other	5.105
r_scbond_it	5.104
r_mcangle_it	4.802
r_mcangle_other	4.801
r_mcbond_it	3.594
r_mcbond_other	3.593
r_angle_other_deg	3.511
r_angle_refined_deg	1.215
r_chiral_restr	0.051
r_bond_refined_d	0.009
r_gen_planes_other	0.005
r_gen_planes_refined	0.004
r_bond_other_d
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	5378
Nucleic Acid Atoms	163
Solvent Atoms	308
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing