2O5E | pdb_00002o5e

Structure of E. coli topoisomerase III in complex with an 8-base single stranded oligonucleotide. Frozen in glucose pH 7.0

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1D6M	PDB ENTRY 1D6M, 1I7D
experimental model	PDB	1I7D	PDB ENTRY 1D6M, 1I7D

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	295	1.5 M (NH4)SO4, 0.1M Sodium citrate, 0.5 NaCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
3.8	67.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 102.26	α = 90
b = 102.26	β = 90
c = 445.61	γ = 90

Symmetry
Space Group	P 43 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	CCD	MARMOSAIC 225 mm CCD		2003-01-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 5ID-B	0.9479	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	2.5	29.132	96.5	0.06	0.06	8.7	4		79675

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)
	2.5	2.56	93		0.328	0.328	2.3	2.5	5552

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1D6M, 1I7D	2.5	29.132	79661	3992	95.74	0.219	0.217	0.21	0.26	0.25	RANDOM	45.063

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]
0.55			0.55		-1.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.846
r_dihedral_angle_4_deg	18.858
r_dihedral_angle_3_deg	16.878
r_dihedral_angle_1_deg	5.635
r_scangle_it	2.22
r_scbond_it	1.354
r_angle_refined_deg	1.247
r_mcangle_it	1.019
r_mcbond_it	0.599
r_nbtor_refined	0.304

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.846
r_dihedral_angle_4_deg	18.858
r_dihedral_angle_3_deg	16.878
r_dihedral_angle_1_deg	5.635
r_scangle_it	2.22
r_scbond_it	1.354
r_angle_refined_deg	1.247
r_mcangle_it	1.019
r_mcbond_it	0.599
r_nbtor_refined	0.304
r_nbd_refined	0.209
r_symmetry_vdw_refined	0.172
r_symmetry_hbond_refined	0.167
r_xyhbond_nbd_refined	0.146
r_chiral_restr	0.084
r_bond_refined_d	0.01
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10062
Nucleic Acid Atoms	276
Solvent Atoms	147
Heterogen Atoms	11

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
CCP4	data scaling
AMoRE	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 R01GM157729.