3RAF | pdb_00003raf

Quinazolinedione-DNA cleavage complex of type IV topoisomerase from S. pneumoniae

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	304	50 mM sodium cacodylate, 5-6% isopropanol, optimised mixture of salts, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 304K

Crystal Properties
Matthews coefficient	Solvent content
4.13	70.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 158.55	α = 90
b = 158.55	β = 90
c = 210.33	γ = 120

Symmetry
Space Group	P 31 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	CCD	ADSC QUANTUM 315		2010-08-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9762	Diamond	I04

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	2.71	114.977	99.9	0.239	0.239	8.6	6	83475	83426			66.392

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)
1	2.71	2.78	100		1.936	0.4	6.1	6122

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	3.24	114.977	1.44	49022	49022	1505	99.77	0.1681	0.1681	0.1668	0.1642	0.2064	0.2025	RANDOM

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]
0.1955			0.1955		-18.9756

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	18.003
f_angle_d	1.283
f_chiral_restr	0.075
f_bond_d	0.009
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10403
Nucleic Acid Atoms	730
Solvent Atoms	40
Heterogen Atoms	56

Software

Software
Software Name	Purpose
GDE	data collection
PHASER	phasing
PHENIX	refinement
xia2	data reduction
xia2	data scaling

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.