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Crystal Structure of XIAP-BIR3 domain in complex with Smac-mimetic compuond, Smac005
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 8.4 293 15% PEG 8000, pH 8.4, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.18 61.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.39 α = 90 b = 92.39 β = 90 c = 175.151 γ = 90
Symmetry Space Group P 41 21 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 CCD MARMOSAIC 225 mm CCD 2007-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.873 ESRF ID23-2
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 3.1 40 99.9 0.199 10.4 6.9 15897 14452
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) 3.1 99.9 0.71 2.7 7.2 2054
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 (All) 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 PDB entry 3CLX 3.1 40 15897 13674 725 99.99 0.23644 0.23644 0.23322 0.2316 0.29985 0.2944 RANDOM 41.912
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] 1.34 1.34 -2.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.315 r_dihedral_angle_3_deg 20.468 r_dihedral_angle_4_deg 15.228 r_dihedral_angle_1_deg 8.236 r_scangle_it 1.374 r_angle_refined_deg 1.359 r_mcangle_it 0.814 r_scbond_it 0.776 r_mcbond_it 0.431 r_symmetry_hbond_refined 0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.315 r_dihedral_angle_3_deg 20.468 r_dihedral_angle_4_deg 15.228 r_dihedral_angle_1_deg 8.236 r_scangle_it 1.374 r_angle_refined_deg 1.359 r_mcangle_it 0.814 r_scbond_it 0.776 r_mcbond_it 0.431 r_symmetry_hbond_refined 0.35 r_nbtor_refined 0.314 r_nbd_refined 0.226 r_symmetry_vdw_refined 0.226 r_xyhbond_nbd_refined 0.143 r_chiral_restr 0.11 r_metal_ion_refined 0.02 r_bond_refined_d 0.009 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 3295 Nucleic Acid Atoms Solvent Atoms 17 Heterogen Atoms 220
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing