6ZT3

N-terminal 47 kDa fragment of the Mycobacterium smegmatis DNA Gyrase B subunit complexed with ADPNP

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3ZKB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	NULL

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.985	α = 90
b = 76.985	β = 90
c = 261.476	γ = 120

Symmetry
Space Group	P 61 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		2019-07-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

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	1.56	65.37	100	0.141	0.143	0.023	1	16.7	38.8		66509			19.9

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	1.56	1.59	100		2.486	2.518	0.399	0.845		39.5

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	3ZKB	1.56	64.69	63082	3287	99.99	0.1493	0.1469	0.1939	RANDOM	23.46

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]
-1.84	-0.92		-1.84		5.98

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.84
r_dihedral_angle_4_deg	18.378
r_dihedral_angle_3_deg	15.125
r_dihedral_angle_1_deg	6.279
r_rigid_bond_restr	3.043
r_angle_other_deg	1.44
r_angle_refined_deg	1.368
r_chiral_restr	0.068
r_bond_refined_d	0.007
r_bond_other_d	0.007

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.84
r_dihedral_angle_4_deg	18.378
r_dihedral_angle_3_deg	15.125
r_dihedral_angle_1_deg	6.279
r_rigid_bond_restr	3.043
r_angle_other_deg	1.44
r_angle_refined_deg	1.368
r_chiral_restr	0.068
r_bond_refined_d	0.007
r_bond_other_d	0.007
r_gen_planes_refined	0.006
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3033
Nucleic Acid Atoms
Solvent Atoms	302
Heterogen Atoms	57

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.