8C41 | pdb_00008c41

High resolution structure of the Streptococcus pneumoniae topoisomerase IV-DNA complex with the novel fluoroquinolone Delafloxacin

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3RAE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	300	2.5% Tacsimate, 50 mM Na Cacodylate, 62.5 mM KCl, 7.5 mM MgCl2, 4-7.5% Isopropanol. 30% MPD as cryoprotectant

Crystal Properties
Matthews coefficient	Solvent content
4.24	71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 157.471	α = 90
b = 157.471	β = 90
c = 212.339	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		2022-10-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.95373	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	2.393	115.01	96.3	0.564	0.569	0.073	1	8.4	60.8		70836		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	2.394	2.689	84		4.363	4.483	0.62	0.83	1.8	49.5

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	2.393	115.01	70682	3458	58.857	0.195	0.1922	0.2	0.2432	0.25	51.207

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]
-0.489	-0.244		-0.489		1.586

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.252
r_dihedral_angle_6_deg	15.192
r_dihedral_angle_2_deg	8.023
r_dihedral_angle_1_deg	7.653
r_lrange_it	6.982
r_lrange_other	6.972
r_mcangle_it	4.711
r_mcangle_other	4.71
r_scangle_it	4.067
r_scangle_other	4.067
r_mcbond_it	2.83
r_mcbond_other	2.829
r_scbond_it	2.386
r_scbond_other	2.386
r_angle_refined_deg	1.54
r_angle_other_deg	0.477
r_nbd_other	0.231
r_nbd_refined	0.22
r_symmetry_nbd_refined	0.214
r_symmetry_nbd_other	0.196
r_xyhbond_nbd_refined	0.186
r_nbtor_refined	0.182
r_symmetry_xyhbond_nbd_refined	0.163
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.071
r_symmetry_xyhbond_nbd_other	0.03
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11462
Nucleic Acid Atoms	732
Solvent Atoms	418
Heterogen Atoms	92

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB-REDO	refinement
DIALS	data reduction
xia2	data reduction
Aimless	data scaling
STARANISO	data scaling
PHASER	phasing