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Crystal structure of XIAP-BIR3 in complex with a bivalent compound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CLX BIR3 DOMAIN FROM PDB ENTRY 3CLX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 4.6 293 20% PEG MME 2000, 60mM sodium acetate tri-hydrate, 120mM Ammonium sulfate, 400mM sodium-potassium tartrate tetra-hydrate, pH 4.6, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.83 67.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.077 α = 90 b = 119.077 β = 90 c = 105.59 γ = 120
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 315 Liquid nitrogen cooled channel-cut silicon monochromator and a cylindrical grazing incidence mirror 2007-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.976 ESRF ID29
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 3 40 0.101 3.6 33440
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) 3 0.64 2.2 3.7 4861
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 BIR3 DOMAIN FROM PDB ENTRY 3CLX 3 40 33415 1688 99.79 0.235 0.231 0.2427 0.311 0.3163 RANDOM 72.888
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] 2.66 1.33 2.66 -4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.397 r_dihedral_angle_3_deg 21.837 r_scangle_it 16.96 r_dihedral_angle_4_deg 12.595 r_scbond_it 12.204 r_mcangle_it 7.383 r_dihedral_angle_1_deg 4.985 r_mcbond_it 4.609 r_angle_refined_deg 2.042 r_chiral_restr 0.122
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.397 r_dihedral_angle_3_deg 21.837 r_scangle_it 16.96 r_dihedral_angle_4_deg 12.595 r_scbond_it 12.204 r_mcangle_it 7.383 r_dihedral_angle_1_deg 4.985 r_mcbond_it 4.609 r_angle_refined_deg 2.042 r_chiral_restr 0.122 r_bond_refined_d 0.011 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6533 Nucleic Acid Atoms Solvent Atoms 505 Heterogen Atoms 552
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling