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Crystal structure of p63 tetramerization domain in complex with darpin 8F1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ZUV 3zuv, 4a9z experimental model PDB 4A9Z 3zuv, 4a9z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293.15 25% PEG3350, 0.2 M sodium chloride, 0.1 M bis-tris pH 5.5
Crystal Properties Matthews coefficient Solvent content 2.29 46.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.563 α = 80.93 b = 50.761 β = 79.92 c = 65.858 γ = 68.75
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 X 16M 2021-03-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.00003 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.27 47.06 92.6 0.065 0.076 0.038 0.997 11.3 3.8 21523
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.27 2.35 91.5 0.542 0.628 0.318 0.9 3.9
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 3zuv, 4a9z 2.27 47.06 20456 1065 92.56 0.1896 0.1872 0.1966 0.2349 0.2415 RANDOM 63.288
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] -3.37 0.27 1.08 3 2.06 0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.613 r_dihedral_angle_4_deg 23.749 r_dihedral_angle_3_deg 16.184 r_dihedral_angle_1_deg 6.039 r_angle_refined_deg 1.244 r_angle_other_deg 1.228 r_chiral_restr 0.063 r_bond_refined_d 0.011 r_gen_planes_refined 0.011 r_gen_planes_other 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.613 r_dihedral_angle_4_deg 23.749 r_dihedral_angle_3_deg 16.184 r_dihedral_angle_1_deg 6.039 r_angle_refined_deg 1.244 r_angle_other_deg 1.228 r_chiral_restr 0.063 r_bond_refined_d 0.011 r_gen_planes_refined 0.011 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3508 Nucleic Acid Atoms Solvent Atoms 51 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing