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Crystal structure of Bcl-2 in complex with the novel orally active inhibitor S55746
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2W3L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.25 284 0.1 M sodium acetate buffer pH 5.25, 20% Jeffamine600, 10% PEG3350
Crystal Properties Matthews coefficient Solvent content 1.76 29.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.09 α = 90 b = 46.9 β = 90 c = 85.04 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 PIXEL DECTRIS PILATUS3 S 6M 2016-11-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.97857 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.39 42.5 98.9 0.034 0.039 0.019 0.999 19.5 4.2 28969
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.39 1.42 91.7 0.54 0.63 0.31 0.877 2.2 3.7
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 (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 2W3L 1.4 20 26743 1447 99.2 0.17904 0.17818 0.1786 0.19439 0.1956 RANDOM 23.1
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 -0.62 -0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.067 r_dihedral_angle_4_deg 17.262 r_dihedral_angle_3_deg 16.35 r_long_range_B_refined 8.336 r_long_range_B_other 8.334 r_dihedral_angle_1_deg 5.36 r_scangle_other 5.316 r_scbond_it 3.54 r_scbond_other 3.538 r_mcangle_other 3.297
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.067 r_dihedral_angle_4_deg 17.262 r_dihedral_angle_3_deg 16.35 r_long_range_B_refined 8.336 r_long_range_B_other 8.334 r_dihedral_angle_1_deg 5.36 r_scangle_other 5.316 r_scbond_it 3.54 r_scbond_other 3.538 r_mcangle_other 3.297 r_mcangle_it 3.284 r_mcbond_it 2.29 r_mcbond_other 2.252 r_angle_refined_deg 1.82 r_angle_other_deg 1.139 r_chiral_restr 0.09 r_bond_refined_d 0.015 r_gen_planes_refined 0.01 r_bond_other_d 0.001 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 1188 Nucleic Acid Atoms Solvent Atoms 151 Heterogen Atoms 53
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing