9NX4 | pdb_00009nx4

Crystal Structure of a P. Aeruginosa Gyrase Chimera In Complex with 20mer DNA and Ciprofloxacin

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		coordinates from apo structure being co-deposited

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	294	0.1M sodium citrate pH 6.0 14% PEG 4000 200mM Ammonium Sulfate 1mM MnCl2 1mM ciprofloxacin

Crystal Properties
Matthews coefficient	Solvent content
3.39	63.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 179.033	α = 90
b = 179.033	β = 90
c = 163.298	γ = 120

Symmetry
Space Group	P 63 2 2

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		2021-10-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.000	APS	22-ID

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	2.85	50	99.2	0.168	0.174	0.043	0.992	3.7	15.5		36343			51.72

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	2.85	2.9			1.252	1.296	0.327	0.815	1.29

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.85	43.67	1.35	36096	1800	98.57	0.2065	0.205	0.2049	0.2344	0.2337	58.3

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	17.3859
f_angle_d	0.9544
f_chiral_restr	0.0524
f_plane_restr	0.0088
f_bond_d	0.0078

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5674
Nucleic Acid Atoms	407
Solvent Atoms	16
Heterogen Atoms	85

Software

Software
Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing