3M6Z

Crystal structure of an N-terminal 44 kDa fragment of topoisomerase V in the presence of guanidium hydrochloride

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	303	0.1 M phosphate citrate pH 5.5, 0.15M sodium sulfate, 0.01M MgCl2, 1 M guanidium hydrochloride, 28% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 303K

Crystal Properties
Matthews coefficient	Solvent content
1.98	37.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.64	α = 90
b = 80.11	β = 90
c = 137.22	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	78	CCD	RAYONIX MX-225	beryllium lenses	2008-07-24	M	SINGLE WAVELENGTH
2	1	x-ray	78	CCD	RAYONIX MX-225		2008-07-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97872	APS	21-ID-G
2	SYNCHROTRON	APS BEAMLINE 21-ID-D	0.97915	APS	21-ID-D

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	1.4	28.9	98.8	0.048	0.045	27.5	8.5	138158	136662

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)
	1.4	1.46	95.5		0.405	0.379	5.3	7.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.4	28.9	136662	129802	6859	98.68	0.16587	0.16491	0.18424	RANDOM	11.181

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]
0.52			-0.32		-0.2

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.878
r_dihedral_angle_4_deg	18.476
r_dihedral_angle_3_deg	12.794
r_dihedral_angle_1_deg	4.709
r_scangle_it	2.181
r_scbond_it	1.651
r_angle_refined_deg	1.195
r_angle_other_deg	0.901
r_mcangle_it	0.892
r_mcbond_it	0.778
r_symmetry_vdw_refined	0.266
r_symmetry_vdw_other	0.242
r_nbd_refined	0.225
r_nbd_other	0.202
r_nbtor_refined	0.177
r_mcbond_other	0.175
r_symmetry_hbond_refined	0.146
r_xyhbond_nbd_refined	0.138
r_nbtor_other	0.082
r_chiral_restr	0.072
r_bond_refined_d	0.009
r_gen_planes_refined	0.006
r_gen_planes_other	0.003
r_bond_other_d	0.002
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6056
Nucleic Acid Atoms
Solvent Atoms	573
Heterogen Atoms	52

Software

Software
Software Name	Purpose
MD2-microdiffractometer	data collection
SHARP	phasing
REFMAC	refinement
XDS	data reduction
SCALA	data scaling