6Y8O

Mycobacterium smegmatis GyrB 22kDa ATPase sub-domain in complex with novobiocin

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.6	293	Crystals grown with 17 mg/ml protein in the presence of 1 mM novobiocin against 15% (w/v) PEG8000, 100 mM sodium acetate pH 5.6, 200 mM calcium acetate were harvested in the precipitant supplemented with 25% (v/v) ethylene glycol for cryoprotection.

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 156.962	α = 90
b = 56.112	β = 90.66
c = 50.678	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	PIXEL	DECTRIS PILATUS 6M		2018-03-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.9159	Diamond	I04-1

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	1.6	78.48	100	0.11	0.119	0.046	0.999	10.4	6.6		58273

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	1.6	1.63	100		1.071	1.159	0.44	0.647		6.8

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	4B6C	1.6	78.48	55300	2973	99.95	0.1367	0.134	0.188	RANDOM	21.903

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]
-1.78		-0.27	0.39		1.4

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.331
r_dihedral_angle_4_deg	16.154
r_dihedral_angle_3_deg	12.131
r_dihedral_angle_1_deg	6.015
r_rigid_bond_restr	2.672
r_angle_refined_deg	1.514
r_angle_other_deg	1.428
r_chiral_restr	0.076
r_bond_refined_d	0.011
r_gen_planes_refined	0.007

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.331
r_dihedral_angle_4_deg	16.154
r_dihedral_angle_3_deg	12.131
r_dihedral_angle_1_deg	6.015
r_rigid_bond_restr	2.672
r_angle_refined_deg	1.514
r_angle_other_deg	1.428
r_chiral_restr	0.076
r_bond_refined_d	0.011
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2931
Nucleic Acid Atoms
Solvent Atoms	389
Heterogen Atoms	141

Software

Software
Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
DIALS	data reduction
PHASER	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 R01GM133198.