7DQJ

E. coli GyrB ATPase domain in complex with 3,4-Dihydroxyacetophenone

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5Z9B

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		298	0.1 M Tris-HCl pH 7.5, 2.20 M (NH4)2HPO4, 10 mM 2-aminobenzimidazole

Crystal Properties
Matthews coefficient	Solvent content
2.57	52.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.46	α = 90
b = 67.462	β = 90
c = 102.5	γ = 90

Symmetry
Space Group	P 21 21 21

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		2019-04-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL19U1	0.97853	SSRF	BL19U1

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	1.92	56.35	99.7	0.98	22.526	6.5		33267

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	1.92	1.99			0.944

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5Z9B	1.92	56.35	31554	1661	99.57	0.23685	0.23548	0.26306	RANDOM	34.753

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]
0.21			1.54		-1.75

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.662
r_dihedral_angle_3_deg	11.311
r_dihedral_angle_4_deg	8.188
r_dihedral_angle_1_deg	4.818
r_angle_other_deg	3.802
r_long_range_B_refined	3.15
r_long_range_B_other	3.083
r_mcangle_it	1.44
r_mcangle_other	1.44
r_scangle_other	1.237
r_angle_refined_deg	1.048
r_mcbond_it	0.811
r_mcbond_other	0.811
r_scbond_it	0.72
r_scbond_other	0.719
r_chiral_restr	0.059
r_bond_refined_d	0.006
r_gen_planes_refined	0.003
r_gen_planes_other	0.002
r_bond_other_d
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2861
Nucleic Acid Atoms
Solvent Atoms	112
Heterogen Atoms	47

Software

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