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Crystal structure of p63 DNA binding domain in complex with inhibitory DARPin G4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3US0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 295 25% PEG 3350
0.2M Li2SO4
0.1M HEPES
Crystal Properties Matthews coefficient Solvent content 2.62 52.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.578 α = 90 b = 96.578 β = 90 c = 77.071 γ = 120
Symmetry Space Group P 31 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 2021-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0 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 1.8 48.29 96.4 0.012 0.027 0.019 0.999 23 1.9 37301
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 1.8 1.84 0.316 0.447 0.316 0.826 1.9
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3US0 1.8 48.29 37299 1865 95.99 0.199 0.1967 0.1961 0.2488 0.2494 40.609
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] 0.398 0.199 0.398 -1.293
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.801 r_dihedral_angle_3_deg 13.484 r_dihedral_angle_4_deg 12.889 r_lrange_other 7.492 r_lrange_it 7.488 r_dihedral_angle_1_deg 7.25 r_scangle_it 5.954 r_scangle_other 5.952 r_mcangle_it 4.894 r_mcangle_other 4.892
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.801 r_dihedral_angle_3_deg 13.484 r_dihedral_angle_4_deg 12.889 r_lrange_other 7.492 r_lrange_it 7.488 r_dihedral_angle_1_deg 7.25 r_scangle_it 5.954 r_scangle_other 5.952 r_mcangle_it 4.894 r_mcangle_other 4.892 r_scbond_it 4.139 r_scbond_other 4.138 r_mcbond_it 3.715 r_mcbond_other 3.713 r_angle_refined_deg 1.606 r_angle_other_deg 1.356 r_nbd_other 0.21 r_nbd_refined 0.205 r_symmetry_nbd_other 0.177 r_nbtor_refined 0.16 r_symmetry_nbd_refined 0.159 r_symmetry_xyhbond_nbd_refined 0.158 r_xyhbond_nbd_refined 0.145 r_chiral_restr 0.08 r_symmetry_nbtor_other 0.077 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2679 Nucleic Acid Atoms Solvent Atoms 186 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement PHASER phasing BUCCANEER model building Coot model building Aimless data scaling xia2 data reduction