3M6K

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

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	303	0.1 M phosphate-citrate pH 5, 0.2 M NaCl, 16% PEG 8000, 1M Guanidium hydrochloride, VAPOR DIFFUSION, HANGING DROP, temperature 303K

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.09	α = 90
b = 70.09	β = 90
c = 349.63	γ = 90

Symmetry
Space Group	P 41 21 2

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	2008-04-23	M	SINGLE WAVELENGTH
2	1	x-ray	78	CCD	RAYONIX MX-225		2008-04-23	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	2.6	29.5	99.9	0.079	0.074	19	8.1	28160	28151			42.1

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)
	2.6	2.72	100		0.572	0.522	3.2	6	3331

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.6	29.14	28151	26710	1438	99.96	0.24371	0.24371	0.24132	0.28883	RANDOM	55.918

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]
2.02			2.02		-4.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.326
r_dihedral_angle_4_deg	18.828
r_dihedral_angle_3_deg	17.444
r_dihedral_angle_1_deg	5.538
r_scangle_it	1.464
r_angle_refined_deg	1.203
r_scbond_it	0.968
r_angle_other_deg	0.89
r_mcangle_it	0.58
r_mcbond_it	0.522
r_symmetry_vdw_other	0.263
r_nbd_refined	0.226
r_symmetry_vdw_refined	0.202
r_nbd_other	0.185
r_nbtor_refined	0.179
r_symmetry_hbond_refined	0.16
r_xyhbond_nbd_refined	0.15
r_mcbond_other	0.086
r_nbtor_other	0.085
r_chiral_restr	0.067
r_bond_refined_d	0.011
r_gen_planes_refined	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	5967
Nucleic Acid Atoms
Solvent Atoms	30
Heterogen Atoms	15

Software

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