3Q8K | pdb_00003q8k

Crystal Structure of Human Flap Endonuclease FEN1 (WT) in complex with product 5'-flap DNA, SM3+, and K+

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7	288	16% mPEG 2k, 20% saturated KCl, 0.5 mM Sm2(SO4)3, 10 mM Mg(NO3)2, 100 mM Hepes pH 7.0, 5% ethylene glycol, VAPOR DIFFUSION, temperature 288K

Crystal Properties
Matthews coefficient	Solvent content
3.41	63.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 105.438	α = 90
b = 105.438	β = 90
c = 105.064	γ = 120

Symmetry
Space Group	P 31 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	CCD	MARMOSAIC 325 mm CCD		2010-04-01		SINGLE WAVELENGTH
2	1	x-ray	90	CCD	ADSC QUANTUM 315r		2010-03-01		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.9796	SSRL	BL11-1
2	SYNCHROTRON	ALS BEAMLINE 12.3.1	1.116	ALS	12.3.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	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	2.2	34.462	99.1	0.083	0.083	7.5	3.6	34291	34291	2	2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.2	2.32	100		0.557	0.557	0.6	3.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	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	PDB ENTRY 1RXW	2.2001	34.46	0.99	63390	34291	3236	95.55	0.1702	0.1679	0.16	0.2126	0.2

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]
4.0229			4.0229		-8.0458

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	19.282
f_angle_d	0.864
f_chiral_restr	0.053
f_bond_d	0.012
f_plane_restr	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2691
Nucleic Acid Atoms	732
Solvent Atoms	568
Heterogen Atoms	6

Software

Software
Software Name	Purpose
SCALA	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
MOSFLM	data reduction

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.