6H1V | pdb_00006h1v

The crystal structure of Pol2CORE in complex with DNA and an incoming nucleotide, carrying an Fe-S cluster

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4M8O

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	291	20% PEG-3350, 50 mM Hepes-NaOH pH 7.0, 10 mM MgCl2, 400 mM LiAc, and 10 mM 2-aminoethanesulfonic acid (taurine)
2	VAPOR DIFFUSION, HANGING DROP	7	291	20% PEG-3350, 50 mM Hepes-NaOH pH 7.0, 10 mM MgCl2, 400 mM LiAc, and 10 mM 2-aminoethanesulfonic acid (taurine)

Crystal Properties
Matthews coefficient	Solvent content
2.53	51.35
2.53	51.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 148.21	α = 90
b = 70.04	β = 109.43
c = 149.93	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	90	PIXEL	DECTRIS PILATUS3 6M		2017-07-13	M	SINGLE WAVELENGTH
2	1	x-ray	90	PIXEL	DECTRIS PILATUS3 6M		2017-11-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.98400	ESRF	ID23-1
2	SYNCHROTRON	ESRF BEAMLINE ID23-1	1.73598	ESRF	ID23-1

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	2.7	73.04	98.6	0.152	0.186	0.106	0.972	5.1	2.9		39543			57.09

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	2.7	2.81	97.5		1.654	2.046	1.188	0.144		2.7

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	THROUGHOUT	4m8o	2.7	19.99	1.33	39250	1956	97.96	0.24	0.2386	0.24	0.2659	0.27	64.9752

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]

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8428
Nucleic Acid Atoms	529
Solvent Atoms	6
Heterogen Atoms	39

Software

Software
Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
Aimless	data scaling
PDB_EXTRACT	data extraction
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.