6Y8L | pdb_00006y8l

Mycobacterium thermoresistibile GyrB21 in complex with novobiocin

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4B6C

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 100 mM zinc chloride, 100 mM ammonium acetate, 3.5-5% (w/v) PEG6000, 3.5-5% (w/v) PEG8000, 3.5-5% (w/v) PEG1000 and 100 mM Bis-Tris pH 7.0-7.3

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.962	α = 90
b = 51.114	β = 100.32
c = 83.205	γ = 90

Symmetry
Space Group	P 1 21 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		2018-07-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9700	Diamond	I03

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	1.4	81.86	100	0.048	0.052	0.02	0.999	15.7	6.5		71663

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	1.4	1.42	100		0.875	0.956	0.38	0.849		6.2

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4B6C	1.4	81.86	67991	3649	99.96	0.142	0.1399	0.1493	0.1813	0.1882	RANDOM	24.977

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]
1.03		0.16	-0.97		-0.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.144
r_dihedral_angle_4_deg	18.797
r_dihedral_angle_3_deg	12.427
r_dihedral_angle_1_deg	5.969
r_rigid_bond_restr	2.579
r_angle_refined_deg	1.513
r_angle_other_deg	1.432
r_chiral_restr	0.077
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2817
Nucleic Acid Atoms
Solvent Atoms	296
Heterogen Atoms	147

Software

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