9N26 | pdb_00009n26

DNA gyrase complexed with uncleaved DNA and Compound 148 to 1.96 A resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7MVS

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.2	298	15% PEG 5000 MME, 0.1M Bis-Tris pH 6.2

Crystal Properties
Matthews coefficient	Solvent content
3	59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 92.937	α = 90
b = 92.937	β = 90
c = 405.763	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 PILATUS3 6M		2022-12-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97911	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	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	1.96	30	99.6	0.135	0.049	18.4	8.9		139668

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.96	2	97.1		1.491	0.808

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	1.963	29.697	139668	7060	99.358	0.173	0.1705	0.1749	0.2167	0.2183	50.514

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]
-0.03	-0.015		-0.03		0.098

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.963
r_dihedral_angle_3_deg	13.628
r_lrange_it	8.636
r_lrange_other	8.636
r_dihedral_angle_2_deg	8.234
r_scangle_it	7.542
r_scangle_other	7.541
r_dihedral_angle_1_deg	6.342
r_scbond_it	5.248
r_scbond_other	5.248
r_mcangle_it	4.786
r_mcangle_other	4.786
r_mcbond_it	3.784
r_mcbond_other	3.782
r_angle_refined_deg	1.937
r_angle_other_deg	0.534
r_dihedral_angle_other_2_deg	0.258
r_symmetry_nbd_refined	0.243
r_symmetry_xyhbond_nbd_refined	0.237
r_nbd_refined	0.21
r_symmetry_nbd_other	0.179
r_nbtor_refined	0.179
r_xyhbond_nbd_refined	0.167
r_nbd_other	0.155
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.076
r_symmetry_xyhbond_nbd_other	0.011
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10630
Nucleic Acid Atoms	797
Solvent Atoms	603
Heterogen Atoms	36

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing