7NGS | pdb_00007ngs

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
2.58	52.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 120.778	α = 90
b = 120.778	β = 90
c = 33.651	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 PILATUS 6M		2018-05-03	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)	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	2.5	42.7	100	0.999	21.1	12		9148

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	2.5	2.6			0.987	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	5NIO	2.5	42.7	8616	479	99.75	0.2036	0.2007	0.21	0.2528	0.25	RANDOM	42.83

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]
2.44			2.44		-4.89

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.354
r_dihedral_angle_4_deg	22.033
r_dihedral_angle_3_deg	18.16
r_dihedral_angle_1_deg	6.112
r_mcangle_it	4.602
r_mcbond_it	3.216
r_mcbond_other	3.207
r_angle_other_deg	2.312
r_angle_refined_deg	1.634
r_chiral_restr	0.093

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.354
r_dihedral_angle_4_deg	22.033
r_dihedral_angle_3_deg	18.16
r_dihedral_angle_1_deg	6.112
r_mcangle_it	4.602
r_mcbond_it	3.216
r_mcbond_other	3.207
r_angle_other_deg	2.312
r_angle_refined_deg	1.634
r_chiral_restr	0.093
r_bond_other_d	0.035
r_gen_planes_other	0.034
r_gen_planes_refined	0.016
r_bond_refined_d	0.014

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1502
Nucleic Acid Atoms
Solvent Atoms	27
Heterogen Atoms	15

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.