6VGG | pdb_00006vgg

Crystal structure of the DNA binding domains of human transcription factor ERG, human Runx2 bound to core binding factor beta (Cbfb), and mithramycin, in complex with 16mer DNA CAGAGGATGTGGCTTC

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		294	0.3 M K/Na Tartrate, 50 mM Hepes, pH 7.0, soaked in 1 mM mithramycin-Mg

Crystal Properties
Matthews coefficient	Solvent content
4.09	69.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 104.678	α = 90
b = 104.678	β = 90
c = 322.836	γ = 120

Symmetry
Space Group	P 62 2 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 EIGER2 X 16M		2018-02-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.000	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	4.3	50	98.3	0.086	28.6	15.7		7632

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	4.3	4.37	93.5		0.871	0.934

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-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	6VGE	4.31	35	7214	372	98.14	0.2531	0.2514	0.2846	RANDOM	287.314

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]
4.46	2.23		4.46		-14.46

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.03
r_dihedral_angle_3_deg	16.897
r_dihedral_angle_4_deg	14.18
r_dihedral_angle_1_deg	6.206
r_angle_refined_deg	1.192
r_angle_other_deg	1.122
r_chiral_restr	0.041
r_bond_other_d	0.005
r_bond_refined_d	0.003
r_gen_planes_refined	0.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.03
r_dihedral_angle_3_deg	16.897
r_dihedral_angle_4_deg	14.18
r_dihedral_angle_1_deg	6.206
r_angle_refined_deg	1.192
r_angle_other_deg	1.122
r_chiral_restr	0.041
r_bond_other_d	0.005
r_bond_refined_d	0.003
r_gen_planes_refined	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2705
Nucleic Acid Atoms	656
Solvent Atoms	2
Heterogen Atoms	152

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	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.