7B24 | pdb_00007b24

DtxR-like iron-dependent regulator IdeR (P39G variant) complexed with cobalt and its consensus 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
3.69	66.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 196.395	α = 90
b = 113.841	β = 117.25
c = 89.795	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		2020-04-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX IV BEAMLINE BioMAX	0.97624	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	2.05	54.93	93.1	0.082	0.088	0.033	0.998	12	7		76685

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	2.05	2.23	61.6		1.305	1.411	0.532	0.573	1.7	6.9

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	2.05	54.93	72891	3794	70.14	0.2273	0.2257	0.2589	RANDOM	51.319

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]
0.01		-0.05	-0.06		0.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	25.756
r_dihedral_angle_4_deg	14.622
r_dihedral_angle_3_deg	12.139
r_dihedral_angle_1_deg	4.784
r_angle_refined_deg	1.099
r_angle_other_deg	1.094
r_chiral_restr	0.038
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	25.756
r_dihedral_angle_4_deg	14.622
r_dihedral_angle_3_deg	12.139
r_dihedral_angle_1_deg	4.784
r_angle_refined_deg	1.099
r_angle_other_deg	1.094
r_chiral_restr	0.038
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	6921
Nucleic Acid Atoms	1189
Solvent Atoms	192
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.