1I7D | pdb_00001i7d

NONCOVALENT COMPLEX OF E.COLI DNA TOPOISOMERASE III WITH AN 8-BASE SINGLE-STRANDED DNA OLIGONUCLEOTIDE

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1D6M	PDB entry 1D6M

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	295	1.3M ammonium sulfate, 0.8M sodium chloride, 0.1M sodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
3.03	59.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 122.011	α = 90
b = 60.831	β = 90.73
c = 125.358	γ = 90

Symmetry
Space Group	C 1 2 1

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	MARRESEARCH		2000-06-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 5ID-B	0.9948	APS	5ID-B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.05	29.63	96.2	0.098	9	5.5	5.3	296621	55797			25.7

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)
	2.05	2.1	96.9		0.244	20.7	2.7	3.5	4129

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 (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1D6M	2.05	29.63	55797	55797	2823	96.1	0.233	0.233	0.233	0.26	RANDOM	47.8

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]
-4.69		-5.46	-11.79		16.48

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	22.1
c_scangle_it	3.75
c_scbond_it	2.62
c_mcangle_it	2.52
c_mcbond_it	1.71
c_angle_deg	1.2
c_improper_angle_d	0.85
c_bond_d	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4933
Nucleic Acid Atoms	158
Solvent Atoms	332
Heterogen Atoms	6

Software

Software
Software Name	Purpose
AMoRE	phasing
CNS	refinement
XDS	data reduction
CCP4	data scaling