8BP2 | pdb_00008bp2

2.8A STRUCTURE OF ZOLIFLODACIN WITH S.AUREUS DNA GYRASE AND DNA

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5CDM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE	6.3	293	90 mM bistris pH 6.3, 9% PEG 5000MME

Crystal Properties
Matthews coefficient	Solvent content
3.28	62.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 94.542	α = 90
b = 94.542	β = 90
c = 417.134	γ = 120

Symmetry
Space Group	P 61

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 S 9M		2022-08-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.9999	Diamond	I24

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.78	25	100	0.997	5.9	18.5		52704

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.78	2.83			0.318

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	FOURIER SYNTHESIS	THROUGHOUT	5CDM	2.8	24.854	51323	2538	99.405	0.193	0.1908	0.19	0.2314	0.23	92.396

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]
2.23	1.115		2.23		-7.233

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.114
r_dihedral_angle_4_deg	17.035
r_dihedral_angle_3_deg	16.392
r_lrange_it	12.356
r_dihedral_angle_1_deg	5.768
r_scangle_it	4.387
r_mcangle_it	3.131
r_scbond_it	2.739
r_mcbond_it	1.817
r_angle_refined_deg	1.722

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.114
r_dihedral_angle_4_deg	17.035
r_dihedral_angle_3_deg	16.392
r_lrange_it	12.356
r_dihedral_angle_1_deg	5.768
r_scangle_it	4.387
r_mcangle_it	3.131
r_scbond_it	2.739
r_mcbond_it	1.817
r_angle_refined_deg	1.722
r_nbtor_refined	0.32
r_symmetry_nbd_refined	0.253
r_nbd_refined	0.221
r_xyhbond_nbd_refined	0.18
r_symmetry_xyhbond_nbd_refined	0.167
r_chiral_restr	0.114
r_bond_refined_d	0.009
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10545
Nucleic Acid Atoms	801
Solvent Atoms	227
Heterogen Atoms	130

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
DIALS	data scaling
PHENIX	phasing

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.