7QFN | pdb_00007qfn

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	Other	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
2.22	44.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 103.021	α = 90
b = 103.021	β = 90
c = 66.693	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		2021-07-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9796	Diamond	I03

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	2.62	89.22	100	0.997	9	10.8		12596

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	2.62	2.74	100		0.78	1.7	11

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	D_1292119290	2.621	89.219	12583	540	99.929	0.202	0.1993	0.21	0.2588	0.26	60.189

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]
1.796	0.898		1.796		-5.826

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	18.251
r_dihedral_angle_6_deg	16.099
r_dihedral_angle_2_deg	9.812
r_lrange_it	9.424
r_lrange_other	9.423
r_dihedral_angle_1_deg	9.256
r_scangle_it	7.576
r_scangle_other	7.557
r_mcangle_other	6.243
r_mcangle_it	6.242
r_scbond_it	5.215
r_scbond_other	5.179
r_mcbond_it	4.398
r_mcbond_other	4.396
r_angle_refined_deg	1.935
r_angle_other_deg	0.641
r_symmetry_xyhbond_nbd_refined	0.358
r_nbd_refined	0.236
r_symmetry_nbd_other	0.206
r_nbd_other	0.19
r_nbtor_refined	0.187
r_xyhbond_nbd_refined	0.167
r_symmetry_nbd_refined	0.148
r_symmetry_nbtor_other	0.094
r_chiral_restr	0.083
r_symmetry_xyhbond_nbd_other	0.032
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_metal_ion_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2886
Nucleic Acid Atoms
Solvent Atoms	13
Heterogen Atoms	38

Software

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