7XV6 | pdb_00007xv6

Crystal structure of the Human TR4 DNA-Binding Domain with C-terminal extension (DBD-CTE) 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		277	PEG 8000, Tris, ammonium sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.69	54.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.146	α = 90
b = 52.146	β = 90
c = 242.701	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		2021-06-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL18U1	0.9793	SSRF	BL18U1

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	2.297	50	96.3	0.998	20.2	7.1		15386

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	2.297	2.36			0.853

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-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3DZU	2.3	31.53	13569	683	85.2	0.188	0.2	0.215	0.2	31.95

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]
-0.037			-0.037		0.074

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.265
r_dihedral_angle_4_deg	17.773
r_dihedral_angle_3_deg	15.901
r_dihedral_angle_1_deg	7.711
r_scangle_it	5.626
r_scangle_other	5.625
r_mcangle_other	5.081
r_mcangle_it	5.08
r_scbond_it	3.761
r_scbond_other	3.761
r_mcbond_it	3.36
r_mcbond_other	3.351
r_angle_refined_deg	1.904
r_angle_other_deg	1.523
r_nbd_other	0.295
r_nbd_refined	0.197
r_nbtor_refined	0.197
r_xyhbond_nbd_refined	0.175
r_chiral_restr	0.085
r_gen_planes_refined	0.011
r_bond_refined_d	0.01
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1226
Nucleic Acid Atoms	732
Solvent Atoms	264
Heterogen Atoms	4

Software

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