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Crystal structure of XIAP-BIR3 with ALP1 series SMAC mimetic ligand
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CLX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 0.05-0.2 M HEPES, pH 8.0, 3.0-3.4 M sodium chloride
Crystal Properties Matthews coefficient Solvent content 5.28 76.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.235 α = 90 b = 71.235 β = 90 c = 105.55 γ = 90
Symmetry Space Group P 41 2 2
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 2023-02-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.9537 Australian Synchrotron MX2
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 2.74 45.46 99.6 0.13 0.133 0.026 0.996 16.5 25.4 7616 72.23
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 2.74 2.87 97.4 1.516 1.548 0.309 0.846 24.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.74 42.41 1.34 7571 359 99.42 0.2023 0.2015 0.2014 0.2191 0.219 75.61
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 24.6917 f_angle_d 1.0296 f_chiral_restr 0.0497 f_bond_d 0.008 f_plane_restr 0.0067
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 839 Nucleic Acid Atoms Solvent Atoms 11 Heterogen Atoms 21
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing