3L2C | pdb_00003l2c

Crystal Structure of the DNA Binding Domain of FOXO4 Bound to DNA

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2UZK	PDB ENTRY 2UZK

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.3	292	HEPES, MgCl2, PEG MME, pH 7.3, vapor diffusion, hanging drop, temperature 292K, VAPOR DIFFUSION, HANGING DROP

Crystal Properties
Matthews coefficient	Solvent content
2.39	48.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 40.81	α = 90
b = 71.7	β = 90
c = 131.86	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	MAR scanner 345 mm plate		2007-11-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	ENRAF-NONIUS FR591

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	1.868	65.938	96.6	0.044	0.044	12.2	7	16689	16135		1

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)
	1.868	1.96	81.6		0.251	0.251	3	6.5	1953

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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2UZK	1.868	19	16083	807	97.79	0.195	0.193	0.1916	0.228	0.2254	RANDOM	21.875

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]
-0.41			0.17		0.24

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	22.784
r_dihedral_angle_4_deg	8.219
r_dihedral_angle_3_deg	6.87
r_scangle_it	2.829
r_scbond_it	2.009
r_angle_refined_deg	1.924
r_mcangle_it	1.874
r_dihedral_angle_1_deg	1.592
r_mcbond_it	1.234
r_nbtor_refined	0.3
r_nbd_refined	0.185
r_symmetry_hbond_refined	0.175
r_symmetry_vdw_refined	0.164
r_xyhbond_nbd_refined	0.138
r_chiral_restr	0.109
r_metal_ion_refined	0.039
r_bond_refined_d	0.013
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	697
Nucleic Acid Atoms	527
Solvent Atoms	163
Heterogen Atoms	2

Software

Software
Software Name	Purpose
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
MOSFLM	data reduction