7JSA | pdb_00007jsa

Crystal structure of the DNA binding domain of human transcription factor ERF in the reduced form, in complex with double-stranded DNA ACCGGAAGTG

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6JVT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.8	294	6% PEG 4000, 0.1M Hepes, 7.8

Crystal Properties
Matthews coefficient	Solvent content
3.44	64.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.798	α = 90
b = 63.798	β = 90
c = 137.502	γ = 90

Symmetry
Space Group	P 41 21 2

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		2018-02-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.00	APS	22-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.85	50	99.9	0.09	32	10.8		7139

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.85	2.9			0.44	0.89	2.06

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	6JVT	2.85	37.75	6712	359	99.28	0.2483	0.2469	0.2512	0.2753	0.2819	RANDOM	84.67

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]
-2.03			-2.03		4.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.882
r_dihedral_angle_4_deg	19.968
r_dihedral_angle_3_deg	18.21
r_dihedral_angle_1_deg	6.472
r_angle_other_deg	1.237
r_angle_refined_deg	1.149
r_chiral_restr	0.053
r_gen_planes_refined	0.006
r_bond_refined_d	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	759
Nucleic Acid Atoms	403
Solvent Atoms	1
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing