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Crystal structure of human TFAP2A in complex with DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Structure of TFAP2A apo-form solved in this study
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 34% v/v PEG 200 , 0.1 M Citric acid pH 3.5
Crystal Properties Matthews coefficient Solvent content 3.89 68.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.261 α = 90 b = 124.261 β = 90 c = 96.926 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 PILATUS3 6M 2022-09-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97930 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 47.04 100 0.096 0.999 23.8 20.2 50700
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 0.952
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 (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.1 19.9 48079 2528 99.83 0.16634 0.16479 0.1743 0.19555 0.2005 RANDOM 35.415
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
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.548 r_dihedral_angle_4_deg 13.954 r_dihedral_angle_3_deg 13.273 r_long_range_B_refined 7.989 r_long_range_B_other 7.966 r_scangle_other 6.561 r_dihedral_angle_1_deg 5.693 r_scbond_it 4.687 r_scbond_other 4.687 r_mcangle_it 4.268
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.548 r_dihedral_angle_4_deg 13.954 r_dihedral_angle_3_deg 13.273 r_long_range_B_refined 7.989 r_long_range_B_other 7.966 r_scangle_other 6.561 r_dihedral_angle_1_deg 5.693 r_scbond_it 4.687 r_scbond_other 4.687 r_mcangle_it 4.268 r_mcangle_other 4.268 r_mcbond_it 3.379 r_mcbond_other 3.378 r_angle_refined_deg 1.808 r_angle_other_deg 1.492 r_chiral_restr 0.094 r_bond_refined_d 0.013 r_gen_planes_refined 0.012 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 3226 Nucleic Acid Atoms 527 Solvent Atoms 303 Heterogen Atoms 88
Software Software Software Name Purpose REFMAC refinement XDS data reduction autoPROC data scaling PHASER phasing