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Crystal structure of the human FoxA2 bound to the TGTTTATT site (forkhead motif ATAAACA)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7YZE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 277 25% PEG 3350, 0.1 M Bis-Tris pH 5.5
Crystal Properties Matthews coefficient Solvent content 2.52 51.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.459 α = 90 b = 92.695 β = 90 c = 116.842 γ = 90
Symmetry Space Group C 2 2 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 PILATUS 6M 2020-02-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.979260 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) 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 2.179 58.421 86.5 0.018 0.998 19.9 9.9 9215
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.179 2.378 52.2 0.544 0.593
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 (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 7YZE 2.18 58.42 8314 901 69.23 0.2254 0.22188 0.2335 0.25728 0.2728 RANDOM 72.04
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] 0.74 -0.19 -0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.494 r_dihedral_angle_1_deg 21.203 r_dihedral_angle_3_deg 15.634 r_dihedral_angle_4_deg 14.097 r_long_range_B_other 7.002 r_long_range_B_refined 7 r_scangle_other 4.943 r_mcangle_it 4.548 r_mcangle_other 4.546 r_scbond_it 3.508
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.494 r_dihedral_angle_1_deg 21.203 r_dihedral_angle_3_deg 15.634 r_dihedral_angle_4_deg 14.097 r_long_range_B_other 7.002 r_long_range_B_refined 7 r_scangle_other 4.943 r_mcangle_it 4.548 r_mcangle_other 4.546 r_scbond_it 3.508 r_scbond_other 3.498 r_mcbond_it 3.05 r_mcbond_other 3.03 r_angle_other_deg 1.337 r_angle_refined_deg 1.173 r_chiral_restr 0.083 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 726 Nucleic Acid Atoms 656 Solvent Atoms 5 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction Aimless data scaling PHENIX phasing