8QMB | pdb_00008qmb

Nucleant-assisted 2.0 A resolution structure of the Streptococcus pneumoniae topoisomerase IV-V18mer DNA complex with the novel fluoroquinolone Delafloxacin

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8C41

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	301	2.5% Tacsimate, 50 mM Na Cacodylate, 62.5 mM KCl, 7.5 mM MgCl2, 5.5-7.0% Isopropanol, 0.05 mg/mL PEGylated graphene as a nucleant. 30% MPD as cryoprotectant and 1 mM beta-mercaptoethanol in the mother liquor.

Crystal Properties
Matthews coefficient	Solvent content
4.22	71.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 157.215	α = 90
b = 157.215	β = 90
c = 211.948	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 EIGER2 XE 16M		2023-03-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9537	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.997	83.768	96.6	0.239	0.24	0.024	1	19	100.1		115609		2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.997	2.306	82		2.948	2.966	0.326	0.827	2.5	82.3

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2	83.628	115602	5806	56.762	0.171	0.1687	0.1687	0.2064	0.2063	47.121

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]
-0.007	-0.004		-0.007		0.023

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.884
r_dihedral_angle_3_deg	15.625
r_dihedral_angle_2_deg	12
r_lrange_it	10.302
r_lrange_other	10.301
r_scangle_it	8.374
r_scangle_other	8.374
r_dihedral_angle_1_deg	8.082
r_mcangle_it	6.532
r_mcangle_other	6.532
r_scbond_it	5.72
r_scbond_other	5.72
r_mcbond_other	4.382
r_mcbond_it	4.381
r_dihedral_angle_other_2_deg	3.953
r_angle_refined_deg	2.26
r_angle_other_deg	0.864
r_symmetry_xyhbond_nbd_refined	0.226
r_nbd_refined	0.208
r_symmetry_nbd_refined	0.208
r_xyhbond_nbd_refined	0.176
r_nbtor_refined	0.174
r_symmetry_nbd_other	0.158
r_nbd_other	0.136
r_chiral_restr	0.117
r_ncsr_local_group_1	0.1
r_symmetry_nbtor_other	0.078
r_metal_ion_refined	0.04
r_symmetry_xyhbond_nbd_other	0.029
r_bond_refined_d	0.012
r_gen_planes_refined	0.012
r_bond_other_d	0.003
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11512
Nucleic Acid Atoms	732
Solvent Atoms	1059
Heterogen Atoms	134

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
xia2	data scaling
STARANISO	data scaling
PHASER	phasing