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Structure of human Bcl-xL in complex with small molecule inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YXJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 284 3.0 M Na Formate, 0.1 M Na Acetate buffer pH 5.5
Crystal Properties Matthews coefficient Solvent content 2.1 40.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.77 α = 90 b = 67.5 β = 96.72 c = 59.88 γ = 90
Symmetry Space Group P 1 21 1
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 6M 2015-11-04 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) 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 2.6 44.6 97.5 0.133 6.6 2.8 8118
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 2.6 2.75 95.2 0.959 1.1 2.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.7 20 6865 398 97.73 0.24093 0.23824 0.2476 0.28588 0.3007 RANDOM 62.407
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] -4.69 -0.35 9.46 -4.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 23.25 r_dihedral_angle_2_deg 20.608 r_long_range_B_refined 16.497 r_long_range_B_other 16.496 r_scangle_other 9.288 r_mcangle_it 8.402 r_mcangle_other 8.4 r_scbond_it 5.587 r_scbond_other 5.581 r_dihedral_angle_1_deg 5.284
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 23.25 r_dihedral_angle_2_deg 20.608 r_long_range_B_refined 16.497 r_long_range_B_other 16.496 r_scangle_other 9.288 r_mcangle_it 8.402 r_mcangle_other 8.4 r_scbond_it 5.587 r_scbond_other 5.581 r_dihedral_angle_1_deg 5.284 r_mcbond_it 5.247 r_mcbond_other 5.242 r_angle_other_deg 1.652 r_angle_refined_deg 1.248 r_chiral_restr 0.057 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_dihedral_angle_4_deg 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 2261 Nucleic Acid Atoms Solvent Atoms 3 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement SCALA data scaling XDS data reduction MOLREP phasing