8J0Q

Structure of DNA binding domain of human TFAP2B

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Structure of TFAP2A solved in this study

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	0.2 M Sodium citrate tribasic dihydrate and 20% PEG 3350 (w/v)

Crystal Properties
Matthews coefficient	Solvent content
2.33	47.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.212	α = 90
b = 81.829	β = 90
c = 115.628	γ = 90

Symmetry
Space Group	P 21 21 21

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 S 9M		2022-09-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL02U1	0.97915	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	2.4	43.41	97.2	0.995	12.9	6.5		19146

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	2.4	2.49			0.97

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.4	38.36	18118	978	97.12	0.18681	0.18385	0.24112	RANDOM	45.962

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]
0.01			-0.02		0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.053
r_dihedral_angle_4_deg	18.681
r_dihedral_angle_3_deg	16.786
r_long_range_B_other	8.667
r_long_range_B_refined	8.665
r_scangle_other	6.725
r_dihedral_angle_1_deg	6.545
r_mcangle_it	5.7
r_mcangle_other	5.699
r_scbond_it	4.559
r_scbond_other	4.557
r_mcbond_it	3.902
r_mcbond_other	3.901
r_angle_refined_deg	1.605
r_angle_other_deg	1.313
r_chiral_restr	0.077
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3005
Nucleic Acid Atoms
Solvent Atoms	57
Heterogen Atoms	12

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing