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Crystal structure of XIAP-BIR2 domain with AIAV 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 1.89 34.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.889 α = 90 b = 74.889 β = 90 c = 109.022 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 1.3 38 100 0.039 30.5 12.6 38399
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 1.3 1.37 100 0.451 5.7 12.8
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 1.3 37.98 38399 36397 2001 99.94 0.17447 0.17347 0.1824 0.19324 0.1958 RANDOM 21.006
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 -0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.03 r_dihedral_angle_4_deg 13.203 r_dihedral_angle_3_deg 12.967 r_dihedral_angle_1_deg 5.32 r_scbond_it 2.035 r_mcangle_it 1.863 r_angle_refined_deg 1.52 r_mcbond_it 1.255 r_mcbond_other 1.232 r_angle_other_deg 0.795
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.03 r_dihedral_angle_4_deg 13.203 r_dihedral_angle_3_deg 12.967 r_dihedral_angle_1_deg 5.32 r_scbond_it 2.035 r_mcangle_it 1.863 r_angle_refined_deg 1.52 r_mcbond_it 1.255 r_mcbond_other 1.232 r_angle_other_deg 0.795 r_chiral_restr 0.099 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 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 1324 Nucleic Acid Atoms Solvent Atoms 154 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling CNX refinement