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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 4.5 284 2.5 M Na Formate, 0.1 M Na Acetate buffer pH 4.5
Crystal Properties Matthews coefficient Solvent content 2.1 42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.6 α = 90 b = 67.89 β = 96.42 c = 67.4 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 PILATUS 6M 2014-07-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
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 3.34 38.7 89.9 0.184 5.2 2.1 7007
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 3.34 3.43 89.8 0.496 2.3 2
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 3.34 20 6653 319 88.26 0.22229 0.21922 0.2235 0.28643 0.2849 RANDOM 39.502
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] -3.52 0.1 5.4 -1.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 20.049 r_dihedral_angle_3_deg 19.032 r_long_range_B_other 11.109 r_long_range_B_refined 11.106 r_dihedral_angle_1_deg 5.626 r_mcangle_other 5.168 r_mcangle_it 5.167 r_scangle_other 5.054 r_mcbond_it 3.072 r_mcbond_other 3.064
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 20.049 r_dihedral_angle_3_deg 19.032 r_long_range_B_other 11.109 r_long_range_B_refined 11.106 r_dihedral_angle_1_deg 5.626 r_mcangle_other 5.168 r_mcangle_it 5.167 r_scangle_other 5.054 r_mcbond_it 3.072 r_mcbond_other 3.064 r_scbond_it 2.892 r_scbond_other 2.892 r_angle_refined_deg 1.374 r_angle_other_deg 0.483 r_chiral_restr 0.061 r_gen_planes_refined 0.006 r_bond_refined_d 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 4440 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 120
Software Software Software Name Purpose REFMAC refinement XDS data scaling XDS data reduction MOLREP phasing