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Crystal Structure of XIAP BIR3 domain in complex with a Smac-mimetic compound, Smac010
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CLX PDB ENTRY 3CLX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8.5 293 12% PEG 10K, 10% glycerol, 0.1M NaCl, pH 8.5, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.22 61.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.529 α = 90 b = 108.349 β = 90 c = 225.308 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 2007-06-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.931 ESRF ID14-1
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 2.5 40 99.9 0.135 14 6.5 66532 66464
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) 2.5 99.9 0.584 2.8 6.7
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 (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3CLX 2.5 40 63088 3376 99.94 0.22306 0.22306 0.22085 0.26379 0.2571 RANDOM 51.255
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] 3.2 0.2 -3.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.738 r_dihedral_angle_3_deg 19.312 r_dihedral_angle_4_deg 16.003 r_dihedral_angle_1_deg 6.405 r_scangle_it 6.166 r_scbond_it 4.071 r_mcangle_it 3.166 r_mcbond_it 1.722 r_angle_refined_deg 1.281 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.738 r_dihedral_angle_3_deg 19.312 r_dihedral_angle_4_deg 16.003 r_dihedral_angle_1_deg 6.405 r_scangle_it 6.166 r_scbond_it 4.071 r_mcangle_it 3.166 r_mcbond_it 1.722 r_angle_refined_deg 1.281 r_nbtor_refined 0.31 r_nbd_refined 0.211 r_chiral_restr 0.21 r_symmetry_vdw_refined 0.196 r_symmetry_hbond_refined 0.182 r_xyhbond_nbd_refined 0.114 r_metal_ion_refined 0.01 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8344 Nucleic Acid Atoms Solvent Atoms 238 Heterogen Atoms 370
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing