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Crystal structure of XIAP-BIR2 domain with AVPI bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4J3Y pdb entry 4J3Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 292 1.7-1.9 M ammonium sulfate, 125 mM bis-tris propane, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 1.87 34.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.815 α = 90 b = 74.815 β = 90 c = 108.64 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 100 PIXEL DECTRIS PILATUS 6M 2012-10-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA SLS X10SA
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 1.42 38 100 0.047 26.1 12.6 29457
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 1.42 1.5 100 0.476 5.7 13.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 pdb entry 4J3Y 1.42 37.9 29456 27904 1549 99.95 0.17342 0.17206 0.1818 0.19882 0.1951 RANDOM 23.721
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] 0.05 0.05 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.571 r_dihedral_angle_4_deg 16.046 r_dihedral_angle_3_deg 13.491 r_dihedral_angle_1_deg 5.536 r_scbond_it 2.392 r_mcangle_it 2.108 r_angle_refined_deg 1.625 r_mcbond_it 1.469 r_mcbond_other 1.429 r_angle_other_deg 0.839
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.571 r_dihedral_angle_4_deg 16.046 r_dihedral_angle_3_deg 13.491 r_dihedral_angle_1_deg 5.536 r_scbond_it 2.392 r_mcangle_it 2.108 r_angle_refined_deg 1.625 r_mcbond_it 1.469 r_mcbond_other 1.429 r_angle_other_deg 0.839 r_chiral_restr 0.106 r_bond_refined_d 0.015 r_gen_planes_refined 0.01 r_bond_other_d 0.001 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1326 Nucleic Acid Atoms Solvent Atoms 121 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling CNX refinement