7XV8

Crystal structure of the Human TR4 DNA-Binding Domain Homodimer Bound to DR1 Response Element

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3DZU

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		291	PEG4000, sodium citrate, ammonium acetate

Crystal Properties
Matthews coefficient	Solvent content
2.82	56.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.874	α = 90
b = 51.874	β = 90
c = 241.506	γ = 90

Symmetry
Space Group	P 43 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 PILATUS 2M		2019-12-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U	0.9793	SSRF	BL17U

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	3.199	50	90.1	0.984	9.2	5.8		5486

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.199	3.28			0.95

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3DZU	3.199	47.708	5207	269	86.209	0.215	0.213	0.2493	53.473

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]
-0.038			-0.038		0.075

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.514
r_dihedral_angle_3_deg	18.182
r_dihedral_angle_4_deg	12.609
r_lrange_other	9.074
r_lrange_it	9.072
r_dihedral_angle_1_deg	7.995
r_mcangle_other	7.273
r_mcangle_it	7.272
r_scangle_it	6.786
r_scangle_other	6.786
r_mcbond_it	4.724
r_mcbond_other	4.705
r_scbond_it	4.492
r_scbond_other	4.482
r_angle_refined_deg	1.548
r_angle_other_deg	1.54
r_symmetry_xyhbond_nbd_refined	0.302
r_nbd_other	0.294
r_symmetry_nbd_other	0.217
r_nbtor_refined	0.204
r_nbd_refined	0.2
r_xyhbond_nbd_refined	0.161
r_xyhbond_nbd_other	0.13
r_symmetry_nbd_refined	0.127
r_symmetry_nbtor_other	0.075
r_chiral_restr	0.072
r_symmetry_xyhbond_nbd_other	0.028
r_gen_planes_refined	0.008
r_bond_refined_d	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1024
Nucleic Acid Atoms	726
Solvent Atoms	59
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
BALBES	phasing