7XV9 | pdb_00007xv9

Crystal structure of the Human TR4 DNA-Binding Domain

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, SITTING DROP		291	Malonate

Crystal Properties
Matthews coefficient	Solvent content
1.81	32.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 32.229	α = 90
b = 32.229	β = 90
c = 128.043	γ = 90

Symmetry
Space Group	P 41

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		2019-08-31	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	1.599	50	99.6	0.9957	21.2	9.1		17222

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	1.599	1.64			0.933

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	3DZU	1.599	32.031	15931	860	92.515	0.177	0.1764	0.19	0.1805	0.19	16.573

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	24.006
r_dihedral_angle_3_deg	16.731
r_dihedral_angle_4_deg	15.423
r_dihedral_angle_1_deg	6.741
r_lrange_it	5.352
r_lrange_other	5.332
r_scangle_it	4.192
r_scangle_other	4.192
r_scbond_it	2.715
r_scbond_other	2.708
r_mcangle_it	2.475
r_mcangle_other	2.474
r_angle_refined_deg	1.761
r_mcbond_other	1.685
r_mcbond_it	1.683
r_angle_other_deg	1.574
r_nbd_refined	0.231
r_nbd_other	0.231
r_symmetry_nbd_refined	0.197
r_symmetry_nbd_other	0.193
r_xyhbond_nbd_refined	0.172
r_nbtor_refined	0.171
r_symmetry_xyhbond_nbd_refined	0.128
r_chiral_restr	0.091
r_symmetry_nbtor_other	0.087
r_bond_refined_d	0.013
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1183
Nucleic Acid Atoms
Solvent Atoms	132
Heterogen Atoms	4

Software

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