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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 0.1 M KSCN, 0.1 M Na acetate buffer pH 5.0, 20% Peg3350
Crystal Properties Matthews coefficient Solvent content 1.9 36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.7 α = 90 b = 67.95 β = 95.74 c = 67.31 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 2014-05-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 Diamond I03
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 1.6 66.97 71.5 0.041 0.052 0.032 0.997 12.7 2.1 50306
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 1.6 1.64 34.9 0.422 0.568 0.377 0.617 1.5
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 1.7 25 43467 2190 77.38 0.17615 0.17416 0.1826 0.21516 0.2204 RANDOM 26.307
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] -0.24 0.23 1.09 -0.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.562 r_dihedral_angle_2_deg 9.609 r_long_range_B_refined 8.415 r_long_range_B_other 8.408 r_scangle_other 6.252 r_dihedral_angle_1_deg 5.588 r_scbond_it 3.907 r_scbond_other 3.907 r_mcangle_it 3.724 r_mcangle_other 3.723
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.562 r_dihedral_angle_2_deg 9.609 r_long_range_B_refined 8.415 r_long_range_B_other 8.408 r_scangle_other 6.252 r_dihedral_angle_1_deg 5.588 r_scbond_it 3.907 r_scbond_other 3.907 r_mcangle_it 3.724 r_mcangle_other 3.723 r_mcbond_other 2.569 r_mcbond_it 2.568 r_angle_refined_deg 1.785 r_angle_other_deg 0.597 r_chiral_restr 0.084 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 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 4723 Nucleic Acid Atoms Solvent Atoms 185 Heterogen Atoms 116
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction MOLREP phasing