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Fragment-Based Drug Discovery Targeting Inhibitor of Apoptosis Proteins: Compound 21
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OPY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 277 0.1M Hepes-NaOH 7.5, 3.9M NaCl
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.145 α = 90 b = 71.145 β = 90 c = 106.403 γ = 90
Symmetry Space Group P 41 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 CCD RIGAKU SATURN 944 2010-11-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.54
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 2.3 42.6 98 0.04 2.3 2.4 12242
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 2.3 2.42 98.5 0.283 2.8
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 2OPY 2.33 42.6 11126 646 96.1 0.2126 0.20923 0.2095 0.27295 0.2718 RANDOM 44.985
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] 0.22 0.22 -0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.387 r_dihedral_angle_3_deg 17.359 r_dihedral_angle_4_deg 14.062 r_long_range_B_refined 7.573 r_dihedral_angle_1_deg 5.442 r_scbond_it 3.332 r_scbond_other 3.329 r_mcbond_it 2.418 r_angle_refined_deg 1.379 r_angle_other_deg 0.187
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.387 r_dihedral_angle_3_deg 17.359 r_dihedral_angle_4_deg 14.062 r_long_range_B_refined 7.573 r_dihedral_angle_1_deg 5.442 r_scbond_it 3.332 r_scbond_other 3.329 r_mcbond_it 2.418 r_angle_refined_deg 1.379 r_angle_other_deg 0.187 r_chiral_restr 0.113 r_bond_refined_d 0.01 r_bond_other_d 0.003 r_gen_planes_refined 0.001 r_gen_planes_other 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_mcbond_other r_mcangle_it r_mcangle_other r_scangle_it r_scangle_other 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 874 Nucleic Acid Atoms Solvent Atoms 143 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement d*TREK data reduction d*TREK data scaling PHASER phasing