9GEF | pdb_00009gef

Experimental localization of metal-binding sites reveals the role of metal ions in the delafloxacin-stabilized Streptococcus pneumoniae topoisomerase IV DNA cleavage complex

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8QMB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	50 mM sodium cacodylate, 62.5 mM KCl, 7.5 mM MgCl 2 , 2.5% Tacsimate TM Hampton Research, 5.5-7% isopropanol, pH 6.5. The protein crystals were cryoprotected with 50 mM sodium cacodylate pH 6.5, 62.5 mM KCl, 7.5 mM MgCl 2 , 2.5% Tacsimate TM Hampton Research, 1 mM beta-mercaptoethanol and 30% v/v MPD before being flash-cooled in liquid nitrogen and collected in elliptical polyimide sample mounts.

Crystal Properties
Matthews coefficient	Solvent content
4.37	71.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 158.533	α = 90
b = 158.533	β = 90
c = 210.82	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	PIXEL	DECTRIS PILATUS 12M		2023-09-23	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I23	2.75, 3.14, 3.54, 4.35, 4.50 and 5.16	Diamond	I23

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	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	2.37	210.82	100	0.215	0.027	0.999	11.6	59.4		124385

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.37	2.41	100		5.369	0.796	0.204		45

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	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	2.62	79.39	62910	1109	69.46	0.18089	0.18041	0.1888	0.2085	0.2092	RANDOM	48.179

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]
-1.27	-0.63		-1.27		4.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.274
r_dihedral_angle_3_deg	15.526
r_dihedral_angle_1_deg	7.359
r_long_range_B_refined	5.662
r_long_range_B_other	5.662
r_scangle_other	2.883
r_mcangle_it	2.718
r_mcangle_other	2.716
r_scbond_it	2.022
r_scbond_other	2.022
r_mcbond_it	1.564
r_mcbond_other	1.564
r_angle_refined_deg	1.44
r_angle_other_deg	0.455
r_chiral_restr	0.061
r_bond_refined_d	0.013
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11504
Nucleic Acid Atoms	732
Solvent Atoms	108
Heterogen Atoms	110

Software

Software
Software Name	Purpose
PDB-REDO	refinement
PHENIX	refinement
DIALS	data reduction
xia2.multiplex	data scaling
DIMPLE	phasing
STARANISO	data scaling
Coot	model building