7NGX | pdb_00007ngx

Mycobacterium tuberculosis transcriptional regulator EthR with bound inhibitory compound

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		300	PEG based

Crystal Properties
Matthews coefficient	Solvent content
2.64	53.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 122.1	α = 90
b = 122.1	β = 90
c = 33.69	γ = 90

Symmetry
Space Group	P 41 21 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 EIGER2 XE 16M		2019-05-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9762	Diamond	I03

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	1.24	38.64	98.9	1	17.8	11.9		71835

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	1.24	1.26			0.406	1

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	5NIO	1.24	38.64	68218	3556	98.77	0.1865	0.1856	0.19	0.2046	0.21	RANDOM	22.82

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]
0.5			0.5		-1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.547
r_dihedral_angle_4_deg	13.046
r_dihedral_angle_3_deg	10.989
r_dihedral_angle_1_deg	5.388
r_mcangle_it	2.77
r_angle_other_deg	2.364
r_mcbond_it	1.97
r_mcbond_other	1.9
r_angle_refined_deg	1.863
r_chiral_restr	0.093

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.547
r_dihedral_angle_4_deg	13.046
r_dihedral_angle_3_deg	10.989
r_dihedral_angle_1_deg	5.388
r_mcangle_it	2.77
r_angle_other_deg	2.364
r_mcbond_it	1.97
r_mcbond_other	1.9
r_angle_refined_deg	1.863
r_chiral_restr	0.093
r_bond_other_d	0.035
r_gen_planes_other	0.018
r_bond_refined_d	0.015
r_gen_planes_refined	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1499
Nucleic Acid Atoms
Solvent Atoms	205
Heterogen Atoms	21

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
Aimless	data reduction
pointless	data scaling
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 R01GM157729.