8QMC | pdb_00008qmc

High resolution structure of the Streptococcus pneumoniae topoisomerase IV-complex with the V-site 18mer dsDNA and 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		301	2.5% Tacsimate, 50 mM Na Cacodylate, 62.5 mM KCl, 7.5 mM MgCl2, 5.5-7.0% Isopropanol. 30% MPD as cryoprotectant

Crystal Properties
Matthews coefficient	Solvent content
4.21	71.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 157.14	α = 90
b = 157.14	β = 90
c = 211.636	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 EIGER X 16M		2023-03-09	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	2.402	64.862	96.2	0.341	0.349	0.078	0.997	10.3	20.1		60189

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	2.402	2.891	86.2		2.05	2.102	0.459	0.745	2	20.8

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	2.402	64.862	60017	3063	50.895	0.244	0.2413	0.2412	0.2992	0.2996	26.352

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]
-0.546	-0.273		-0.546		1.772

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.89
r_dihedral_angle_6_deg	14.534
r_dihedral_angle_1_deg	8.147
r_dihedral_angle_2_deg	6.664
r_lrange_it	2.356
r_lrange_other	2.353
r_angle_refined_deg	1.382
r_mcangle_it	1.19
r_mcangle_other	1.19
r_scangle_it	0.928
r_scangle_other	0.928
r_mcbond_it	0.705
r_mcbond_other	0.704
r_scbond_it	0.535
r_scbond_other	0.535
r_angle_other_deg	0.449
r_nbd_refined	0.238
r_symmetry_nbd_refined	0.238
r_nbd_other	0.224
r_symmetry_xyhbond_nbd_refined	0.212
r_symmetry_nbd_other	0.202
r_xyhbond_nbd_refined	0.184
r_nbtor_refined	0.183
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.068
r_symmetry_xyhbond_nbd_other	0.022
r_metal_ion_refined	0.01
r_bond_refined_d	0.006
r_gen_planes_refined	0.005
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11512
Nucleic Acid Atoms	732
Solvent Atoms	426
Heterogen Atoms	98

Software

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