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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 5.5 284 0.2 M Ca Acetate, 0.1 M Na Acetate buffer pH 5.5, 10 % PegMME550, 10% Peg3350
Crystal Properties Matthews coefficient Solvent content 1.9 36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.51 α = 90 b = 68.59 β = 96.55 c = 60.06 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 2016-03-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92819 Diamond I04-1
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 1.48 30.6 95.7 0.043 0.053 0.031 0.998 13 2.5 43007
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 1.48 1.52 0.576 0.766 0.5 0.655 1.2 1.9
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.5 25.001 41415 2021 95.735 0.199 0.1975 0.2061 0.2329 0.2395 30.937
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] -0.82 0.271 1.868 -1.082
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.025 r_dihedral_angle_2_deg 14.379 r_dihedral_angle_3_deg 12.854 r_dihedral_angle_other_2_deg 10.311 r_lrange_it 9.131 r_lrange_other 9.129 r_scangle_it 6.114 r_scangle_other 6.112 r_dihedral_angle_1_deg 5.753 r_mcangle_it 4.038
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.025 r_dihedral_angle_2_deg 14.379 r_dihedral_angle_3_deg 12.854 r_dihedral_angle_other_2_deg 10.311 r_lrange_it 9.131 r_lrange_other 9.129 r_scangle_it 6.114 r_scangle_other 6.112 r_dihedral_angle_1_deg 5.753 r_mcangle_it 4.038 r_mcangle_other 4.037 r_scbond_it 4.004 r_scbond_other 4.004 r_mcbond_it 2.882 r_mcbond_other 2.881 r_angle_refined_deg 1.633 r_angle_other_deg 0.583 r_symmetry_nbd_refined 0.373 r_symmetry_xyhbond_nbd_refined 0.368 r_xyhbond_nbd_refined 0.243 r_nbd_refined 0.235 r_nbtor_refined 0.192 r_symmetry_nbd_other 0.187 r_nbd_other 0.185 r_chiral_restr 0.079 r_symmetry_nbtor_other 0.071 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_symmetry_xyhbond_nbd_other 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2311 Nucleic Acid Atoms Solvent Atoms 150 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction MOLREP phasing