7ZBG | pdb_00007zbg

Human Topoisomerase II Beta ATPase ADP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7QFO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.2 M ammonium sulphate, 0.1 M bis tris (pH 5.5), 25 % w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 103.4	α = 90
b = 103.4	β = 90
c = 67.02	γ = 120

Symmetry
Space Group	P 3 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	PIXEL	DECTRIS PILATUS 6M		2022-02-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.99987	Diamond	I24

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	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	2.3	53.714	99.8	0.996	11	19.2		18666

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.38			0.565	1.5

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	7QFO	2.3	53.714	18661	983	99.727	0.201	0.1972	0.2	0.2593	0.26	43.233

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]
0.456	0.228		0.456		-1.479

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	43.198
r_dihedral_angle_3_deg	17.17
r_dihedral_angle_6_deg	15.43
r_lrange_it	10.59
r_lrange_other	10.554
r_dihedral_angle_1_deg	8.326
r_scangle_it	8.108
r_scangle_other	8.106
r_mcangle_it	6.393
r_mcangle_other	6.392
r_scbond_it	5.763
r_scbond_other	5.761
r_mcbond_it	4.542
r_mcbond_other	4.527
r_angle_refined_deg	1.82
r_angle_other_deg	0.587
r_symmetry_nbd_refined	0.295
r_nbd_refined	0.231
r_symmetry_nbd_other	0.198
r_nbd_other	0.192
r_nbtor_refined	0.186
r_xyhbond_nbd_refined	0.184
r_symmetry_xyhbond_nbd_refined	0.169
r_symmetry_nbtor_other	0.088
r_chiral_restr	0.083
r_metal_ion_refined	0.063
r_symmetry_xyhbond_nbd_other	0.06
r_bond_refined_d	0.01
r_gen_planes_refined	0.01
r_chiral_restr_other	0.003
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2909
Nucleic Acid Atoms
Solvent Atoms	50
Heterogen Atoms	68

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
XDS	data reduction
Coot	model building
MolProbity	model building
pointless	data scaling
Aimless	data scaling
MOLREP	phasing