7XVA | pdb_00007xva

Crystal structure of the Human TR4 Ligand Binding Domain in complex with the JAZF1 corepressor fragment

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3P0U

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		291	HEPES, ammonium sulfate, sodium acetate, MPD

Crystal Properties
Matthews coefficient	Solvent content
2.28	45.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.851	α = 90
b = 76.851	β = 90
c = 98.365	γ = 90

Symmetry
Space Group	P 43 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 PILATUS 2M		2021-10-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL02U1	0.9793	SSRF	BL02U1

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	1.856	50	98	0.998	36	9.5		25132

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	1.856	1.9			0.996

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3P0U	1.856	28.09	24001	1248	93.747	0.198	0.1965	0.21	0.2187	0.23	19.405

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]
-0.002			-0.002		0.005

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.434
r_dihedral_angle_4_deg	18.073
r_dihedral_angle_3_deg	15.117
r_dihedral_angle_1_deg	5.947
r_lrange_it	5.799
r_lrange_other	5.662
r_scangle_it	4.204
r_scangle_other	4.203
r_mcangle_it	3.184
r_mcangle_other	3.183
r_scbond_it	2.724
r_scbond_other	2.721
r_mcbond_it	2.035
r_mcbond_other	2.034
r_angle_refined_deg	1.583
r_angle_other_deg	1.429
r_symmetry_nbd_refined	0.356
r_nbd_other	0.242
r_symmetry_xyhbond_nbd_refined	0.219
r_nbd_refined	0.207
r_symmetry_nbd_other	0.18
r_nbtor_refined	0.168
r_xyhbond_nbd_refined	0.132
r_symmetry_nbtor_other	0.084
r_chiral_restr	0.082
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1886
Nucleic Acid Atoms
Solvent Atoms	119
Heterogen Atoms

Software

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