2O54 | pdb_00002o54

Structure of E. coli topoisomerase III in complex with an 8-base single stranded oligonucleotide. Frozen in glycerol at 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, 0.1 M Sodium citrate, 0.5 M NaCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
3.82	67.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 101.83	α = 90
b = 101.83	β = 90
c = 452.38	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	0.9756	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	2.479	29.103	96.8	0.072	0.072	8.4	4.8		82671

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)
	2.48	2.54	75.9		0.262	0.262	2.9	2.7	4688

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	29.103	81830	4104	97.65	0.225	0.222	0.22	0.269	0.26	RANDOM	26.236

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]
-0.05			-0.05		0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.227
r_dihedral_angle_4_deg	19.505
r_dihedral_angle_3_deg	17.131
r_dihedral_angle_1_deg	5.613
r_scangle_it	2.238
r_scbond_it	1.39
r_angle_refined_deg	1.274
r_mcangle_it	0.897
r_mcbond_it	0.533
r_nbtor_refined	0.305

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.227
r_dihedral_angle_4_deg	19.505
r_dihedral_angle_3_deg	17.131
r_dihedral_angle_1_deg	5.613
r_scangle_it	2.238
r_scbond_it	1.39
r_angle_refined_deg	1.274
r_mcangle_it	0.897
r_mcbond_it	0.533
r_nbtor_refined	0.305
r_symmetry_vdw_refined	0.212
r_nbd_refined	0.211
r_symmetry_hbond_refined	0.18
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	10029
Nucleic Acid Atoms	296
Solvent Atoms	211
Heterogen Atoms	2

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.