7NGR | pdb_00007ngr

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
2.62	53.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 121.61	α = 90
b = 121.61	β = 90
c = 33.74	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	1.92	121.61	100	0.998	8.9	12.4		20021

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	1.92	1.95			0.461	0.88

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	1.92	86.14	18962	1015	99.95	0.2103	0.2082	0.22	0.2501	0.25	RANDOM	32.835

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]
1.15			1.15		-2.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.192
r_dihedral_angle_4_deg	22.329
r_dihedral_angle_3_deg	13.489
r_dihedral_angle_1_deg	5.248
r_mcangle_it	3.688
r_mcbond_it	2.646
r_mcbond_other	2.644
r_angle_other_deg	2.317
r_angle_refined_deg	1.637
r_chiral_restr	0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.192
r_dihedral_angle_4_deg	22.329
r_dihedral_angle_3_deg	13.489
r_dihedral_angle_1_deg	5.248
r_mcangle_it	3.688
r_mcbond_it	2.646
r_mcbond_other	2.644
r_angle_other_deg	2.317
r_angle_refined_deg	1.637
r_chiral_restr	0.1
r_gen_planes_other	0.063
r_bond_other_d	0.036
r_gen_planes_refined	0.028
r_bond_refined_d	0.016

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1496
Nucleic Acid Atoms
Solvent Atoms	43
Heterogen Atoms	20

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.