7L19 | pdb_00007l19

Crystal structure of the MarR family transcriptional regulator from Enterobacter soli strain LF7 bound to Indole 3 acetic acid

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7KUA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.1 M Bis-Tris: HCl, pH 6.5, 2 M Ammonium Sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.42	49.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 117.699	α = 90
b = 117.699	β = 90
c = 74.14	γ = 120

Symmetry
Space Group	P 32 2 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 PILATUS3 6M		2020-11-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	1.0332	APS	23-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.76	50	99.1	0.156	0.164	0.052	7.9	9.5		15270

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	2.76	2.81	90		1.234	1.364	0.561	0.653		4.5

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	7KUA	2.77	46.14	14495	765	98.83	0.2356	0.2333	0.23	0.2762	0.27	RANDOM	72.519

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]
0.9	0.45		0.9		-2.91

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.055
r_dihedral_angle_4_deg	19.852
r_dihedral_angle_3_deg	19.279
r_dihedral_angle_1_deg	7.268
r_angle_refined_deg	1.925
r_angle_other_deg	1.509
r_chiral_restr	0.094
r_bond_refined_d	0.015
r_gen_planes_refined	0.009
r_bond_other_d	0.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.055
r_dihedral_angle_4_deg	19.852
r_dihedral_angle_3_deg	19.279
r_dihedral_angle_1_deg	7.268
r_angle_refined_deg	1.925
r_angle_other_deg	1.509
r_chiral_restr	0.094
r_bond_refined_d	0.015
r_gen_planes_refined	0.009
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2754
Nucleic Acid Atoms
Solvent Atoms	4
Heterogen Atoms	40

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

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.