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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 5 284 4.0 M Na Formate, 0.1 M Na Acetate buffer pH 5.0
Crystal Properties Matthews coefficient Solvent content 3.1 60
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.78 α = 90 b = 73.78 β = 90 c = 157.28 γ = 90
Symmetry Space Group P 43 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 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 2.36 25.5 99.1 0.055 22.3 9.3 18437
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 2.36 2.5 95.1 0.587 2.7 9.4
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 2.4 25 16835 839 99.75 0.18839 0.18644 0.1952 0.22796 0.2246 RANDOM 65.63
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] -2.54 -2.54 5.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 19.073 r_dihedral_angle_3_deg 16.739 r_long_range_B_refined 13.876 r_long_range_B_other 13.876 r_scangle_other 10.065 r_mcangle_it 9.217 r_mcangle_other 9.214 r_scbond_other 6.791 r_scbond_it 6.79 r_mcbond_it 6.612
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 19.073 r_dihedral_angle_3_deg 16.739 r_long_range_B_refined 13.876 r_long_range_B_other 13.876 r_scangle_other 10.065 r_mcangle_it 9.217 r_mcangle_other 9.214 r_scbond_other 6.791 r_scbond_it 6.79 r_mcbond_it 6.612 r_mcbond_other 6.586 r_dihedral_angle_1_deg 5.831 r_angle_refined_deg 1.541 r_angle_other_deg 0.551 r_chiral_restr 0.071 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 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 2379 Nucleic Acid Atoms Solvent Atoms 51 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement SCALA data scaling XDS data reduction MOLREP phasing