1QZR

CRYSTAL STRUCTURE OF THE ATPASE REGION OF SACCHAROMYCES CEREVISIAE TOPOISOMERASE II BOUND TO ICRF-187 (DEXRAZOXANE)

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	microbatch under oil	6.5	293	PEG 1500, POTASSIUM CHLORIDE, GLYCEROL, SODIUM CACODYLATE, pH 6.5, microbatch under oil, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.553	α = 90
b = 71.444	β = 90
c = 215.724	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		2002-07-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	1.1271	ALS	8.3.1

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	1.9	50	90.8	0.057	0.057	16.1	3.3	65576	60064			28.34

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)
1	1.9	1.97	59.8		0.298	0.298	3.2	2.1

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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1PVG	1.9	45.18	65576	60064	5512	90.79	0.19911	0.19911	0.19565	0.23741	RANDOM	27.203

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]
2.22			-0.98		-1.24

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.803
r_scangle_it	3.248
r_scbond_it	1.956
r_mcangle_it	1.187
r_angle_refined_deg	1.038
r_mcbond_it	0.609
r_nbd_refined	0.191
r_symmetry_vdw_refined	0.154
r_xyhbond_nbd_refined	0.123
r_symmetry_hbond_refined	0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.803
r_scangle_it	3.248
r_scbond_it	1.956
r_mcangle_it	1.187
r_angle_refined_deg	1.038
r_mcbond_it	0.609
r_nbd_refined	0.191
r_symmetry_vdw_refined	0.154
r_xyhbond_nbd_refined	0.123
r_symmetry_hbond_refined	0.1
r_chiral_restr	0.081
r_bond_refined_d	0.011
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6110
Nucleic Acid Atoms
Solvent Atoms	766
Heterogen Atoms	83

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	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.