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Crystal structure of XIAP-BIR3 in complex with a cIAP1-selective SM
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 EVAPORATION 7.5 293 10% PEG 400, 0.2 M MgCl2, 0.1M Hepes-Na
Crystal Properties Matthews coefficient Solvent content 2.73 54.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.23 α = 90 b = 97.06 β = 90 c = 182.6 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 210 Toroidal focusing mirror 2012-09-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.939 ESRF ID14-4
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.7 66.5 100 0.043 0.136 8 6 28799
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.85 0.718 0.78 4113
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 MOLECULAR REPLACEMENT THROUGHOUT 3CLX 2.7 66.5 27239 1440 99.74 0.23761 0.2351 0.242 0.28408 0.2925 RANDOM 71.01
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] 4.29 2 -6.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.084 r_dihedral_angle_4_deg 20.656 r_dihedral_angle_3_deg 20.091 r_long_range_B_refined 13.364 r_long_range_B_other 13.363 r_mcangle_it 9.854 r_mcangle_other 9.854 r_scangle_other 9.711 r_mcbond_it 6.466 r_mcbond_other 6.463
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.084 r_dihedral_angle_4_deg 20.656 r_dihedral_angle_3_deg 20.091 r_long_range_B_refined 13.364 r_long_range_B_other 13.363 r_mcangle_it 9.854 r_mcangle_other 9.854 r_scangle_other 9.711 r_mcbond_it 6.466 r_mcbond_other 6.463 r_scbond_it 6.249 r_scbond_other 6.248 r_dihedral_angle_1_deg 6.129 r_angle_refined_deg 1.355 r_angle_other_deg 1.249 r_chiral_restr 0.078 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6485 Nucleic Acid Atoms Solvent Atoms 85 Heterogen Atoms 288
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction iMOSFLM data reduction MOLREP phasing