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Crystal structure of XIAP-Bir2 with a bound spirocyclic benzoxazepinone inhibitor.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3J3Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 292 1.5 M ammonium sulfate, 125 mM Bis-tris-propane , pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 1.88 34.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.196 α = 90 b = 74.196 β = 90 c = 108.564 γ = 90
Symmetry Space Group I 4 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 IMAGE PLATE RIGAKU RAXIS HTC 2011-01-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.7 37.7 98.8 0.038 17 4.6 16849
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.76 0.371 2.8 3.16 1664
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 FOURIER SYNTHESIS THROUGHOUT 3J3Y 1.7 37.13 15961 885 98.73 0.19636 0.19415 0.198 0.23789 0.2354 RANDOM 33.403
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] 0.03 0.03 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.382 r_dihedral_angle_4_deg 16.139 r_dihedral_angle_3_deg 14.805 r_dihedral_angle_1_deg 5.497 r_angle_refined_deg 1.748 r_angle_other_deg 0.943 r_chiral_restr 0.109 r_bond_refined_d 0.018 r_gen_planes_refined 0.011 r_bond_other_d 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.382 r_dihedral_angle_4_deg 16.139 r_dihedral_angle_3_deg 14.805 r_dihedral_angle_1_deg 5.497 r_angle_refined_deg 1.748 r_angle_other_deg 0.943 r_chiral_restr 0.109 r_bond_refined_d 0.018 r_gen_planes_refined 0.011 r_bond_other_d 0.005 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_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it 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 1298 Nucleic Acid Atoms Solvent Atoms 100 Heterogen Atoms 42
Software Software Software Name Purpose CrystalClear data collection CCP4 model building REFMAC refinement d*TREK data reduction d*TREK data scaling CCP4 phasing