2B9S | pdb_00002b9s

Crystal Structure of heterodimeric L. donovani topoisomerase I-vanadate-DNA complex

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	9.1	298	18% PEG 3350, 0.2 M Na2HPO4, 0.1 M LiCl, pH 9.1, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.38	63.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.433	α = 90
b = 106.102	β = 90
c = 126.691	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	MARRESEARCH		2005-07-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.97915	SSRL	BL9-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.27	50	95.9	0.073		3.8	43803	43803	1	1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.27	2.35	73	71.6	0.408		2.2

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.27	43.48	43803	43746	2217	100	0.233	0.233	0.231	0.23	0.275	0.27	RANDOM	34.498

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]
-1.57			0.5		1.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.726
r_dihedral_angle_4_deg	16.015
r_dihedral_angle_3_deg	15.234
r_dihedral_angle_1_deg	5.977
r_scangle_it	2.788
r_mcangle_it	2.32
r_scbond_it	1.851
r_angle_refined_deg	1.597
r_mcbond_it	1.491
r_symmetry_hbond_refined	0.352

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.726
r_dihedral_angle_4_deg	16.015
r_dihedral_angle_3_deg	15.234
r_dihedral_angle_1_deg	5.977
r_scangle_it	2.788
r_mcangle_it	2.32
r_scbond_it	1.851
r_angle_refined_deg	1.597
r_mcbond_it	1.491
r_symmetry_hbond_refined	0.352
r_nbtor_refined	0.301
r_symmetry_vdw_refined	0.194
r_nbd_refined	0.191
r_metal_ion_refined	0.185
r_xyhbond_nbd_refined	0.143
r_chiral_restr	0.095
r_bond_refined_d	0.012
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3715
Nucleic Acid Atoms	889
Solvent Atoms	130
Heterogen Atoms	3

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
AMoRE	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.