5Z9P

Bacterial GyrB ATPase domain in complex with a chemical fragment

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4P8O

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		298	0.1M Tris-HCl pH 8.0, 0.1M MgCl2, 22%(w/v) Polyethylene glycol 3,350

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 143.103	α = 90
b = 55.66	β = 100.27
c = 51.055	γ = 90

Symmetry
Space Group	C 1 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	CCD	ADSC QUANTUM 315r		2016-09-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U1	0.979	SSRF	BL17U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.45	70.41	96.1	0.039	41.9	3		67161

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.45	1.5	88.6		0.073		2.7

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	4P8O	1.45	70.4	63865	3296	96	0.193	0.193	0.21	RANDOM	11.11

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]
-0.17		-0.03	-0.06		0.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.544
r_dihedral_angle_4_deg	19.02
r_dihedral_angle_3_deg	9.585
r_dihedral_angle_1_deg	5.386
r_long_range_B_refined	2.778
r_long_range_B_other	2.588
r_scangle_other	1.331
r_angle_refined_deg	1.191
r_mcangle_it	0.914
r_mcangle_other	0.914
r_angle_other_deg	0.872
r_scbond_it	0.852
r_scbond_other	0.851
r_mcbond_it	0.539
r_mcbond_other	0.538
r_chiral_restr	0.073
r_bond_refined_d	0.007
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001
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	2920
Nucleic Acid Atoms
Solvent Atoms	350
Heterogen Atoms	22

Software

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