8RLY | pdb_00008rly

E. coli endonuclease IV complexed with sulfate, catalytic Fe2+

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1QTW

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		295	1 microliter protein mixed with 2 microliter precipitant. Protein: 12.5 mg/ml, 20 mM Tris-HCl pH 8.0, 150 mM NaCl. Precipitant: 0.1 M HEPES pH 7.0, 15% Polyethylene Glycol 3,350, 10 mM Magnesium chloride hexahydrate, 5 mM nickel (II) chloride hexahydrate

Crystal Properties
Matthews coefficient	Solvent content
2.28	46.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.78	α = 90
b = 115.98	β = 90
c = 177.7	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	170	PIXEL	DECTRIS EIGER X 16M		2023-11-29	M	SINGLE WAVELENGTH
2	1	x-ray	170	PIXEL	DECTRIS EIGER X 16M		2023-11-29	M	SINGLE WAVELENGTH
3	1	x-ray	170	PIXEL	DECTRIS EIGER X 16M		2023-11-29	M	SINGLE WAVELENGTH
4	1	x-ray	170	PIXEL	DECTRIS EIGER X 16M		2023-11-29	M	SINGLE WAVELENGTH
5	1	x-ray	170	PIXEL	DECTRIS EIGER X 16M		2023-11-29	M	SINGLE WAVELENGTH
6	1	x-ray	170	PIXEL	DECTRIS EIGER X 16M		2023-11-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	1.7712	Diamond	I03
2	SYNCHROTRON	DIAMOND BEAMLINE I03	1.6984	Diamond	I03
3	SYNCHROTRON	DIAMOND BEAMLINE I03	1.5028	Diamond	I03
4	SYNCHROTRON	DIAMOND BEAMLINE I03	1.4760	Diamond	I03
5	SYNCHROTRON	DIAMOND BEAMLINE I03	1.3051	Diamond	I03
6	SYNCHROTRON	DIAMOND BEAMLINE I03	1.2782	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	1.9	97.12	87.8	0.06475	0.07067	0.998	14.86	5.8		193287			22.18

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	1.9	1.92	21.7		0.3256	0.4496	0.3083	0.772	1.36	1.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1QTW	1.9	97.12	1.35	192678	9776	87.75	0.159	0.1565	0.1559	0.2068	0.2055	23.66

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	14.2939
f_angle_d	0.9674
f_chiral_restr	0.0556
f_plane_restr	0.0113
f_bond_d	0.0096

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10994
Nucleic Acid Atoms
Solvent Atoms	1118
Heterogen Atoms	67

Software

Software
Software Name	Purpose
PHENIX	refinement
xia2	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.