1PVG | pdb_00001pvg

Crystal Structure of the ATPase region of Saccharomyces Cerevisiae topoisomerase II

X-RAY DIFFRACTION

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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
2.31	46.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.456	α = 90
b = 71.081	β = 90
c = 216.132	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		2002-05-16	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	1.127, 0.9796	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	1.8	30	89.5	0.061	0.061	22	6.7	76036	75706			27.502

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	1.8	1.86	72.7		0.43	0.43	2.8	4.9	6077

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	MAD	THROUGHOUT	1.8	29.75	0.43	76036	69319	6385	89.65	0.20866	0.20866	0.20566	0.2064	0.24147	0.2388	RANDOM	23.666

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]
1.93			-1.4		-0.53

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.832
r_scangle_it	2.574
r_scbond_it	1.733
r_angle_refined_deg	0.966
r_mcangle_it	0.861
r_mcbond_it	0.447
r_symmetry_vdw_refined	0.199
r_nbd_refined	0.192
r_symmetry_hbond_refined	0.111
r_xyhbond_nbd_refined	0.107
r_chiral_restr	0.074
r_bond_refined_d	0.009
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6083
Nucleic Acid Atoms
Solvent Atoms	745
Heterogen Atoms	64

Software

Software
Software Name	Purpose
REFMAC	refinement
Blu-Ice	data collection
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	phasing