☰ Navigation Tabs
Structure of DNA binding domain of human TFAP2B
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 (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) 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 0.1901 0.24112 0.2429 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
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