2ZBK

Crystal structure of an intact type II DNA topoisomerase: insights into DNA transfer mechanisms

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1MU5	PDB ENTRY 1MU5, 1MX0
experimental model	PDB	1MX0	PDB ENTRY 1MU5, 1MX0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	293	25mM sodium acetate pH4.6, 50mM ammonium sulphate, 6.6% PEG-MME-2000, 10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
4.48	72.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 114.96	α = 90
b = 200.53	β = 90
c = 329.07	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	CCD	ADSC QUANTUM 4		2006-10-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.9798	ESRF	ID23-1

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	3.5	40	90.4	0.108	8.1	2.7		88994		-3	79.165

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	3.55	3.6	75.6		0.524	0.524	1.9	2.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	PDB ENTRY 1MU5, 1MX0	3.56	19.99	98444	84522	4471	100	0.313	0.313	0.312	0.333	RANDOM	66.325

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]
-5.07			6.77		-1.71

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.74
r_dihedral_angle_3_deg	22.2
r_dihedral_angle_4_deg	17.538
r_dihedral_angle_1_deg	6.523
r_mcangle_it	1.705
r_angle_refined_deg	1.308
r_mcbond_it	0.95
r_scangle_it	0.591
r_symmetry_hbond_refined	0.412
r_symmetry_vdw_refined	0.369

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.74
r_dihedral_angle_3_deg	22.2
r_dihedral_angle_4_deg	17.538
r_dihedral_angle_1_deg	6.523
r_mcangle_it	1.705
r_angle_refined_deg	1.308
r_mcbond_it	0.95
r_scangle_it	0.591
r_symmetry_hbond_refined	0.412
r_symmetry_vdw_refined	0.369
r_scbond_it	0.365
r_nbtor_refined	0.351
r_nbd_refined	0.324
r_xyhbond_nbd_refined	0.298
r_chiral_restr	0.086
r_bond_refined_d	0.012
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	27676
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	100

Software

Software
Software Name	Purpose
XSCALE	data scaling
SHELX	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
SHELXD	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.