7B23 | pdb_00007b23

DtxR-like iron-dependent regulator IdeR complexed with cobalt and the SACE_2689 promoter DNA-binding sequence

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7B1V

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	293	30%(w/v) PEG 2000 MME, 0.2 M ammonium sulfate, 0.1 M sodium acetate

Crystal Properties
Matthews coefficient	Solvent content
3.6	65.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 194.25	α = 90
b = 113.125	β = 117.25
c = 89.288	γ = 90

Symmetry
Space Group	C 1 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 EIGER X 16M		2019-03-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX IV BEAMLINE BioMAX	0.9184	MAX IV	BioMAX

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	2.15	94.63	92.6	0.083	0.09	0.035	0.998	10.9	6.7		59657

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	2.15	2.41	71		0.984	1.066	0.406	0.604	1.6	6.7

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-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	7B1V	2.15	94.63	56713	2944	63.8	0.2274	0.2263	0.2476	RANDOM	58.065

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]
0.25		-0.06	0.27		-0.29

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	26.187
r_dihedral_angle_4_deg	17.54
r_dihedral_angle_3_deg	12.359
r_dihedral_angle_1_deg	5.18
r_angle_refined_deg	1.117
r_angle_other_deg	1.085
r_chiral_restr	0.04
r_bond_refined_d	0.002
r_gen_planes_refined	0.002
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	26.187
r_dihedral_angle_4_deg	17.54
r_dihedral_angle_3_deg	12.359
r_dihedral_angle_1_deg	5.18
r_angle_refined_deg	1.117
r_angle_other_deg	1.085
r_chiral_restr	0.04
r_bond_refined_d	0.002
r_gen_planes_refined	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6956
Nucleic Acid Atoms	1189
Solvent Atoms	50
Heterogen Atoms	8

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	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.