8J0R

Structure of human TFAP2A in complex with DNA

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	0.1 M citric acid (pH3.5), 34% PEG 200 (w/v).

Crystal Properties
Matthews coefficient	Solvent content
3.92	68.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 124.79	α = 90
b = 124.79	β = 90
c = 96.917	γ = 120

Symmetry
Space Group	P 32 2 1

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 EIGER X 16M		2022-12-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL10U2	0.97918	SSRF	BL10U2

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	2.1	108.1	100	0.998	15	9.1		51127

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	2.1	2.16			0.825

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	2.1	19.99	48346	2688	99.8	0.1638	0.16213	0.19411	RANDOM	34.284

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	-0.01		-0.01		0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.979
r_dihedral_angle_4_deg	15.511
r_dihedral_angle_3_deg	13.061
r_long_range_B_refined	8.398
r_long_range_B_other	8.344
r_scangle_other	6.91
r_dihedral_angle_1_deg	5.602
r_scbond_it	4.861
r_scbond_other	4.861
r_mcangle_it	3.994
r_mcangle_other	3.994
r_mcbond_it	3.168
r_mcbond_other	3.165
r_angle_refined_deg	1.789
r_angle_other_deg	1.494
r_chiral_restr	0.095
r_bond_refined_d	0.013
r_gen_planes_refined	0.013
r_gen_planes_other	0.002
r_bond_other_d	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	3243
Nucleic Acid Atoms	527
Solvent Atoms	359
Heterogen Atoms	85

Software

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