3M4A | pdb_00003m4a

Crystal structure of a bacterial topoisomerase IB in complex with DNA reveals a secondary DNA binding site

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2F4Q	PDB entry 2F4Q

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.5	283	30% PEG 400 (w/v), 0.1 M sodium acetate (pH 4.5), 0.2 M calcium chloride. 1:1 molar ratio of protein and DNA, VAPOR DIFFUSION, HANGING DROP, temperature 283K

Crystal Properties
Matthews coefficient	Solvent content
2.65	53.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 119.67	α = 90
b = 53.44	β = 96.33
c = 77.36	γ = 90

Symmetry
Space Group	C 1 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	IMAGE PLATE	MAR scanner 345 mm plate	Franks mirrors	2006-01-01	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	MAR CCD 165 mm		2006-03-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.5418
2	SYNCHROTRON		1.00

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	1.65	76	96.2	0.053	0.048	24.1	4.7	58613	56385

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)
	1.65	1.69	89.5		0.325	0.276	4.1	3.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	PDB entry 2F4Q	1.65	19.824	58613	53565	2820	96.16	0.19487	0.19487	0.19344	0.2	0.22169	0.23	RANDOM	13.658

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]
0.3		0.01	-0.72		0.43

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.368
r_dihedral_angle_3_deg	12.094
r_dihedral_angle_4_deg	11.133
r_dihedral_angle_1_deg	4.818
r_scangle_it	2.479
r_scbond_it	1.743
r_angle_refined_deg	1.29
r_mcangle_it	1.017
r_angle_other_deg	0.947
r_mcbond_it	0.936
r_symmetry_vdw_other	0.242
r_symmetry_hbond_refined	0.233
r_nbd_refined	0.202
r_nbd_other	0.189
r_symmetry_vdw_refined	0.188
r_nbtor_refined	0.185
r_mcbond_other	0.154
r_xyhbond_nbd_refined	0.141
r_nbtor_other	0.078
r_chiral_restr	0.066
r_bond_refined_d	0.008
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2420
Nucleic Acid Atoms	486
Solvent Atoms	281
Heterogen Atoms	9

Software

Software
Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
SCALA	data scaling